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wind: wORKFLOW FOR PiRNAs AnD BEYONd
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EDA hclust_function -- The `x` argument to `enframe()` must be a vector, not hclust. #4

Closed methornton closed 8 months ago

methornton commented 1 year ago

Hello!

I am having some issues with the hclust_function. The EDA script runs without issue up until this point.

here is the error

Error in `map2()`:
ℹ In index: 1.
ℹ With name: salmon.
Caused by error in `enframe()`:
! The `x` argument to `enframe()` must be a vector, not hclust.
Backtrace:
     ▆
  1. ├─purrr::map2(norm_dgls, dat_path, ~function_clust(.x, .y))
  2. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
  3. │   ├─purrr:::with_indexed_errors(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   ├─purrr:::call_with_cleanup(...)
  6. │   └─global .f(.x[[i]], .y[[i]], ...)
  7. │     └─global function_clust(.x, .y)
  8. │       ├─rafalib::myplclust(...)
  9. │       │ ├─base::plot(...)
 10. │       │ └─stats:::plot.hclust(...)
 11. │       │   └─graphics::title(...)
 12. │       │     └─grDevices::as.graphicsAnnot(main)
 13. │       ├─stringr::str_glue("{enframe(list_hc[[i]])$value[7]} - {enframe(list_hc[[i]])$value[5]} - {names(list_hc[i])}")
 14. │       │ └─glue::glue(..., .sep = .sep, .envir = .envir)
 15. │       │   └─glue::glue_data(...)
 16. │       └─tibble::enframe(list_hc[[i]])
 17. │         └─tibble:::abort_enframe_must_be_vector(x)
 18. │           └─tibble:::tibble_abort(...)
 19. │             └─rlang::abort(x, class, ..., call = call, parent = parent, use_cli_format = TRUE)
 20. └─glue (local) `<fn>`("enframe(list_hc[[i]])$value[7]")
 21.   ├─.transformer(expr, env) %||% .null
 22.   └─glue (local) .transformer(expr, env)
 23.     └─base::eval(parse(text = text, keep.source = FALSE), envir)
 24.       └─base::eval(parse(text = text, keep.source = FALSE), envir)
Execution halted

It could be that I don't have enough annotations for these normalization methods, but they are all present with some counts.

ConYel commented 1 year ago

Hello @methornton , could you change in the code the part

pdf(file.path(plot_path, str_glue("hierarchic_clust_{basename(plot_path)}.pdf")))
  for (i in seq_along(list_hc)) {
       rafalib::myplclust(list_hc[[i]],
       lab.col = as.character(dgl_fc$colours),  
       xlab = NULL,
       main = str_glue("{enframe(list_hc[[i]])$value[7]} - {enframe(list_hc[[i]])$value[5]} - {names(list_hc[i])}"))
       legend("topright",
       legend = levels(dgl_fc$samples$group),
       fill = levels(dgl_fc$colours),  
       bty="n",
       cex = 0.9)
       }
  dev.off()
}

comment the main=... which is the title argument for the plot 

pdf(file.path(plot_path, str_glue("hierarchic_clust_{basename(plot_path)}.pdf")))
  for (i in seq_along(list_hc)) {
       rafalib::myplclust(list_hc[[i]],
       lab.col = as.character(dgl_fc$colours),  
       xlab = NULL,
  # main = str_glue("{enframe(list_hc[[i]])$value[7]} - {enframe(list_hc[[i]])$value[5]} - {names(list_hc[i])}"))
       legend("topright",
       legend = levels(dgl_fc$samples$group),
       fill = levels(dgl_fc$colours),  
       bty="n",
       cex = 0.9)
       }
  dev.off()
}

If that works I will try to see why it doesn't work as vector.

methornton commented 1 year ago

Hello! Thank you! So if I comment the line out both of the curly brackets on the bottom turn read and I get an unexpected "{" error. 

 for (i in seq_along(list_hc)) {
+                 rafalib::myplclust(list_hc[[i]],
+                                    lab.col = as.character(dgl_fc$colours),
+                                    xlab = NULL,
+                                    #main = str_glue("{enframe(list_hc[[i]])$value[7]} - {enframe(list_hc[[i]])$value[5]} - {names(list_hc[i])}"))
+                 legend("topright", legend = levels(dgl_fc$samples$group), fill = levels(dgl_fc$colours), bty="n", cex = 0.9)
+         }
Error: unexpected '}' in:
"                legend("topright", legend = levels(dgl_fc$samples$group), fill = levels(dgl_fc$colours), bty="n", cex = 0.9)
        }"
>         dev.off()
null device 
          1 
> }
Error: unexpected '}' in "}"

When I went through again line by line I get a warning about normalization. 

> norm_dgls <- filtered_dgls %>% map2(.y = dat_path, ~function_norm(.x, .y))
Warning messages:                                                             
1: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
2: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
3: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
4: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
> # save the list with all normalized values (edgeR and limma-voom)-----
>   do_not_print <- map2( .x = norm_dgls, .y = dat_path, ~write_rds(.x, file = file.path(.y, str_glue("list_norm_dgls_{basename(.y)}.rds"))))

I don't see any offsets, this is what filtered_dgls contains 

> str(filtered_dgls)
List of 2
 $ salmon:Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. ..$ names: chr [1:3] "counts" "samples" "offset"
 $ fc    :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. ..$ names: chr [1:3] "counts" "samples" "colours"

I appreciate your help.

methornton commented 1 year ago

There is an offset in the salmon data but not in the featureCounts. Where would the offset come from?

> head(filtered_dgls$salmon$offset)
                                             MOE_1_HC1_quan MOE_2_HC2_quan
URS00004F0321_GR_chr1_56410_56481_72_-             11.05509       11.19833
URS000232E62B_GR_chr1_29445616_29445695_80_-       11.05509       11.19833
URS00007E4957_GR_chr1_29445625_29445647_23_-       11.05509       11.19833
> filtered_dgls$fc$colours
 [1] #e41a1c #e41a1c #e41a1c #e41a1c #377eb8 #377eb8 #377eb8 #377eb8 #4daf4a
[10] #4daf4a #4daf4a #4daf4a #984ea3 #984ea3 #984ea3 #984ea3 #ff7f00 #ff7f00
[19] #ff7f00 #ff7f00
Levels: #e41a1c #377eb8 #4daf4a #984ea3 #ff7f00
> head(filtered_dgls$fc$offset)
NULL
methornton commented 1 year ago

I found the list_norm_dgls for both featureCounts and Salmon. Here is what they look like.

> clean <- readRDS("list_norm_dgls_featureCounts.rds")
> str(clean)
List of 10
 $ none           :Loading required package: edgeR
Loading required package: limma
Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. ..$ names: chr [1:3] "counts" "samples" "colours"
 $ TMM            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. ..$ names: chr [1:3] "counts" "samples" "colours"
 $ TMMwsp         :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. ..$ names: chr [1:3] "counts" "samples" "colours"
 $ RLE            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1.13 1.101 0.967 0.846 1.181 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. ..$ names: chr [1:3] "counts" "samples" "colours"
 $ voom_Quantile  :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:609, 1:20] 16.33 11.93 7.21 10.75 11.21 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 13.45 20.56 6.67 13.55 16.31 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voom_TMM       :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 170492 203626 180697 179670 196029 ...
  .. .. .. ..$ norm.factors: num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:609, 1:20] 15 12.02 7.01 10.81 11.16 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 18.71 16.39 6.68 13.52 14.85 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voom_TMMwsp    :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 172773 207700 182453 177621 193473 ...
  .. .. .. ..$ norm.factors: num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:609, 1:20] 15 12 7 10.8 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 18.77 16.28 6.69 13.45 14.77 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_Quantile:Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. ..$ norm.factors  : num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 0.956 1.159 1.651 0.716 2.376 ...
  .. .. ..$ : num [1:609, 1:20] 16.33 11.93 7.21 10.75 11.21 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 15.64 24.21 6.96 15.8 19.15 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_TMM     :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 170492 203626 180697 179670 196029 ...
  .. .. .. ..$ norm.factors  : num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 0.91 1.1 1.715 0.722 2.555 ...
  .. .. ..$ : num [1:609, 1:20] 15 12.02 7.01 10.81 11.16 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 24.37 18.92 6.71 15 16.64 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_TMMwsp  :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 172773 207700 182453 177621 193473 ...
  .. .. .. ..$ norm.factors  : num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 0.928 1.109 1.69 0.717 2.778 ...
  .. .. ..$ : num [1:609, 1:20] 15 12 7 10.8 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:609, 1:20] 23.43 18.89 6.87 15.22 16.81 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"

> clean <- readRDS("list_norm_dgls_salmon.rds")
> str(clean)
List of 10
 $ none           :Loading required package: edgeR
Loading required package: limma
Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. ..$ names: chr [1:3] "counts" "samples" "offset"
 $ TMM            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. ..$ names: chr [1:3] "counts" "samples" "offset"
 $ TMMwsp         :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. ..$ names: chr [1:3] "counts" "samples" "offset"
 $ RLE            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. ..@ .Data:List of 3
  .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 0.975 0.955 0.955 1.062 1.087 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. ..$ names: chr [1:3] "counts" "samples" "offset"
 $ voom_Quantile  :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 13.25 14.26 6.76 10.74 9.2 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 12.24 11.41 1.93 6.24 4.15 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voom_TMM       :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 59698 72249 70815 73330 69984 ...
  .. .. .. ..$ norm.factors: num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 13.3 14.41 6.8 10.65 9.17 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 9.06 8.87 1.81 6.47 4.02 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voom_TMMwsp    :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  6 variables:
  .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size    : num [1:20] 63896 72454 64359 74215 72834 ...
  .. .. .. ..$ norm.factors: num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. ..$ : num [1:234, 1:20] 13.2 14.31 6.7 10.55 9.08 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 10.24 9.96 1.99 6.5 4.15 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_Quantile:Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. ..$ norm.factors  : num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 1.104 1.124 1.652 0.851 1.736 ...
  .. .. ..$ : num [1:234, 1:20] 13.25 14.26 6.76 10.74 9.2 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 15.34 14.37 2.34 7.64 4.72 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_TMM     :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 59698 72249 70815 73330 69984 ...
  .. .. .. ..$ norm.factors  : num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 1.059 1.119 1.605 0.839 1.727 ...
  .. .. ..$ : num [1:234, 1:20] 13.3 14.41 6.8 10.65 9.17 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 10.86 10.62 2.04 7.42 4.35 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ voomQW_TMMwsp  :Formal class 'EList' [package "limma"] with 1 slot
  .. ..@ .Data:List of 4
  .. .. ..$ :'data.frame':  20 obs. of  7 variables:
  .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. ..$ lib.size      : num [1:20] 63896 72454 64359 74215 72834 ...
  .. .. .. ..$ norm.factors  : num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ sample.weights: num [1:20] 1.123 1.163 1.594 0.754 1.776 ...
  .. .. ..$ : num [1:234, 1:20] 13.2 14.31 6.7 10.55 9.08 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ : num [1:234, 1:20] 13.7 13.35 2.4 8 4.88 ...
  .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
methornton commented 1 year ago

Hello! This is what norm_dgls looks like. It looks like it has the data even though the function gave an error message.

> str(norm_dgls)
List of 2
 $ salmon:List of 10
  ..$ none           :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "offset"
  ..$ TMM            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "offset"
  ..$ TMMwsp         :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "offset"
  ..$ RLE            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:234, 1:20] 599.86 1301.56 6.16 95.4 34 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 0.975 0.955 0.955 1.062 1.087 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 11.1 11.1 11.1 11.1 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "offset"
  ..$ voom_Quantile  :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 13.25 14.26 6.76 10.74 9.2 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 12.24 11.41 1.93 6.24 4.15 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voom_TMM       :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 59698 72249 70815 73330 69984 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 13.3 14.41 6.8 10.65 9.17 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 9.06 8.87 1.81 6.47 4.02 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voom_TMMwsp    :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 63896 72454 64359 74215 72834 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:234, 1:20] 13.2 14.31 6.7 10.55 9.08 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 10.24 9.96 1.99 6.5 4.15 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_Quantile:Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 64677 73277 68096 68833 68571 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 1.104 1.124 1.652 0.851 1.736 ...
  .. .. .. ..$ : num [1:234, 1:20] 13.25 14.26 6.76 10.74 9.2 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 15.34 14.37 2.34 7.64 4.72 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_TMM     :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 59698 72249 70815 73330 69984 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 0.923 0.986 1.04 1.065 1.021 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 1.059 1.119 1.605 0.839 1.727 ...
  .. .. .. ..$ : num [1:234, 1:20] 13.3 14.41 6.8 10.65 9.17 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 10.86 10.62 2.04 7.42 4.35 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_TMMwsp  :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 63896 72454 64359 74215 72834 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 0.988 0.989 0.945 1.078 1.062 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 1.123 1.163 1.594 0.754 1.776 ...
  .. .. .. ..$ : num [1:234, 1:20] 13.2 14.31 6.7 10.55 9.08 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:234] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS00007E4957_GR_chr1_29445625_29445647_23_-" "URS0000D50ED3_GR_chr1_29445625_29445685_61_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:234, 1:20] 13.7 13.35 2.4 8 4.88 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
 $ fc    :List of 10
  ..$ none           :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "colours"
  ..$ TMM            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "colours"
  ..$ TMMwsp         :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "colours"
  ..$ RLE            :Formal class 'DGEList' [package "edgeR"] with 1 slot
  .. .. ..@ .Data:List of 3
  .. .. .. ..$ : num [1:609, 1:20] 5589.5 709.3 21.6 306.6 389.7 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1.13 1.101 0.967 0.846 1.181 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : Factor w/ 5 levels "#e41a1c","#377eb8",..: 1 1 1 1 2 2 2 2 3 3 ...
  .. .. ..$ names: chr [1:3] "counts" "samples" "colours"
  ..$ voom_Quantile  :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:609, 1:20] 16.33 11.93 7.21 10.75 11.21 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 13.45 20.56 6.67 13.55 16.31 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voom_TMM       :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 170492 203626 180697 179670 196029 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:609, 1:20] 15 12.02 7.01 10.81 11.16 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 18.71 16.39 6.68 13.52 14.85 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voom_TMMwsp    :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  6 variables:
  .. .. .. .. ..$ group       : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size    : num [1:20] 172773 207700 182453 177621 193473 ...
  .. .. .. .. ..$ norm.factors: num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. .. ..$ sample_name : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set         : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug        : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. ..$ : num [1:609, 1:20] 15 12 7 10.8 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 18.77 16.28 6.69 13.45 14.77 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_Quantile:Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 151088 177012 185882 215271 164337 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 0.956 1.159 1.651 0.716 2.376 ...
  .. .. .. ..$ : num [1:609, 1:20] 16.33 11.93 7.21 10.75 11.21 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 15.64 24.21 6.96 15.8 19.15 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_TMM     :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 170492 203626 180697 179670 196029 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 1.128 1.15 0.972 0.835 1.193 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 0.91 1.1 1.715 0.722 2.555 ...
  .. .. .. ..$ : num [1:609, 1:20] 15 12.02 7.01 10.81 11.16 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 24.37 18.92 6.71 15 16.64 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
  ..$ voomQW_TMMwsp  :Formal class 'EList' [package "limma"] with 1 slot
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ :'data.frame':   20 obs. of  7 variables:
  .. .. .. .. ..$ group         : Factor w/ 5 levels "CTR.Control",..: 1 1 1 1 4 4 4 4 2 2 ...
  .. .. .. .. ..$ lib.size      : num [1:20] 172773 207700 182453 177621 193473 ...
  .. .. .. .. ..$ norm.factors  : num [1:20] 1.144 1.173 0.982 0.825 1.177 ...
  .. .. .. .. ..$ sample_name   : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. ..$ Set           : chr [1:20] "CTR" "CTR" "CTR" "CTR" ...
  .. .. .. .. ..$ Drug          : chr [1:20] "Control" "Control" "Control" "Control" ...
  .. .. .. .. ..$ sample.weights: num [1:20] 0.928 1.109 1.69 0.717 2.778 ...
  .. .. .. ..$ : num [1:609, 1:20] 15 12 7 10.8 11.1 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:609] "URS00004F0321_GR_chr1_56410_56481_72_-" "URS000232E62B_GR_chr1_29445616_29445695_80_-" "URS000075BFA6_GR_chr1_29445625_29445645_21_-" "URS00003F2D94_GR_chr1_29445625_29445646_22_-" ...
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. ..$ : num [1:609, 1:20] 23.43 18.89 6.87 15.22 16.81 ...
  .. .. .. ..$ : num [1:20, 1:5] 1 1 1 1 0 0 0 0 0 0 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:20] "MOE_1_HC1_quan" "MOE_2_HC2_quan" "MOE_3_HC3_quan" "MOE_4_HC4_quan" ...
  .. .. .. .. .. ..$ : chr [1:5] "CTR.Control" "EXP.Ace" "EXP.Lyral" "TRN.Ace" ...
  .. .. .. .. ..- attr(*, "assign")= int [1:5] 1 1 1 1 1
  .. .. .. .. ..- attr(*, "contrasts")=List of 1
  .. .. .. .. .. ..$ targets_file$group: chr "contr.treatment"
  .. .. ..$ names: chr [1:4] "targets" "E" "weights" "design"
ConYel commented 1 year ago

Hello sorry we are probably missing a parentheses in the for loop. try changing to 

pdf(file.path(plot_path, str_glue("hierarchic_clust_{basename(plot_path)}.pdf")))
  for (i in seq_along(list_hc)) {
       rafalib::myplclust(list_hc[[i]],
       lab.col = as.character(dgl_fc$colours),  
       xlab = NULL,
  # main = str_glue("{enframe(list_hc[[i]])$value[7]} - {enframe(list_hc[[i]])$value[5]} - {names(list_hc[i])}"))
)                                                             # <- this 
       legend("topright",
       legend = levels(dgl_fc$samples$group),
       fill = levels(dgl_fc$colours),  
       bty="n",
       cex = 0.9)
       }
  dev.off()
}

That is the one commented out above so myplclust function wasn't properly completed.

methornton commented 1 year ago

Hello!

I added the close parentheses in the spot and the script made 30 hclust images and MDS plots for both featureCounts and salmon, until it gave this error most likely within PCA plots. 

$salmon
null device 
          1 

$fc
null device 
          1 

$salmon
pdf 
  2 

$fc
pdf 
  2 

Error in `map2()`:
ℹ In index: 1.
ℹ With name: salmon.
Caused by error in `if (dgl_norm_data[[norm_method]]$samples$batch[1]) ...`:
! argument is of length zero
Backtrace:
     ▆
  1. ├─purrr::map2(norm_dgls, dat_path, ~function_PCA(.x, .y))
  2. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
  3. │   ├─purrr:::with_indexed_errors(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   ├─purrr:::call_with_cleanup(...)
  6. │   └─global .f(.x[[i]], .y[[i]], ...)
  7. │     └─global function_PCA(.x, .y)
  8. └─base::.handleSimpleError(...)
  9.   └─purrr (local) h(simpleError(msg, call))
 10.     └─cli::cli_abort(...)
 11.       └─rlang::abort(...)
Execution halted

hierarchic_clust_salmon.pdf hierarchic_clust_featureCounts.pdf MDS_plot_salmon.pdf MDS_plot_featureCounts.pdf

ConYel commented 1 year ago

Hello @methornton !

Yes, the problem is that it considers the batch column in order to add it in the PCA. I'll update you in a bit with hopefully a solution

UPDATE

I added a !is,null(...) in the if else condition, could you add it in your code as below and see if it is working?!

if(!is.null(dgl_norm_data[[norm_method]]$samples$batch[1])){
    d$batch <- dgl_norm_data[[norm_method]]$samples$batch %>% as_factor
    p <-  ggplot(data=d, 
                 aes_string(x="PC1", 
                            y="PC2", 
                            color="group", 
                            shape="batch"))
  }else{
methornton commented 1 year ago

Hello! Thank you! It runs and then adds the PCA plots. I am getting an error before the "top100". The script does make the salmon_FC_cpm_union_grouped text file. I changed "top100" to "top10" figuring there were less significant sncRNA, I also changed "piRNA" to "miRNA" thinkng that there may not be enough piRNA, but I'm still getting the same error. I really appreciate your help! Also, it isn't making the PCA plot for voomQW_Quantile analysis, is it supposed to?

Joining with `by = join_by(sncRNA)`
Error in enc2utf8(path) : argument is not a character vector
Calls: %>% ... mutate -> <Anonymous> -> standardise_path -> as.list
Execution halted

PCA_plot_lcpm_TMM_featureCounts.pdf

ConYel commented 1 year ago

Hello @methornton Could you try to run piece by piece the code in order to see if it actually loads properly the datasets?

comp_FC_sal <- map2(norm_dgls, list("_salmon", "_fc"), ~function_comp_groups(.x,.y))

annot_tbl <- file.path("human_data","sncRNA_piRNBnk_RNACent_GRCh38_v34.gtf") %>% 
  read_gff2()

complete_biotypes_seqs <- annot_tbl %>% 
  as_tibble() %>% 
  distinct(gene_id, .keep_all = TRUE) %>% 
  select(!c(seqnames:strand,type:phase)) %>% 
  dplyr::rename("sncRNA" = gene_id)

salmon_FC_cpm_union_grouped <- comp_FC_sal %>% 
  bind_rows(.id = "method") %>% 
  pivot_longer(cols = !c(method,sncRNA)) %>% 
  pivot_wider(names_from = c(name, method),
              values_from = value) %>% 
  left_join(complete_biotypes_seqs) %>%
  select(sncRNA, gene_type, everything()) %>% 
  write_tsv(file.path(dirname(dat_path[1]), "salmon_FC_cpm_union_grouped.txt"))

Is the annot_tbl "genomic ranges"? Is the complete_biotypes_seqs made properly as a tibble/dataframe? Could you check what output has the :

comp_FC_sal %>% 
  bind_rows(.id = "method") %>% 
  pivot_longer(cols = !c(method,sncRNA)) %>% 
  pivot_wider(names_from = c(name, method),
              values_from = value)
methornton commented 1 year ago

Hi @ConYel Sorry I was pulled away to do some bench work. So I am able to get the EDA script to run with the exception of the second part of section 15. Interestingly I get an error which only occurs infrequently. I think it is with package.config. This is the error from the command line. This only happens infrequently.

Filtering out low count features...
897 features are to be kept for differential expression analysis with filtering method 1
Filtering out low count features...
1433 features are to be kept for differential expression analysis with filtering method 3
Error in `map2()`:
ℹ In index: 1.
ℹ With name: salmon.
Caused by error in `map2()`:
ℹ In index: 1.
ℹ With name: counts.
Caused by error in `asNamespace("pkgconfig")$get_config()`:
! attempt to apply non-function
Backtrace:
     ▆
  1. ├─list(salmon = dgl_salmon, fc = dgl_fc) %>% ...
  2. ├─purrr::map2(., .y = dat_path, ~function_filtering(.x, .y))
  3. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
  4. │   ├─purrr:::with_indexed_errors(...)
  5. │   │ └─base::withCallingHandlers(...)
  6. │   ├─purrr:::call_with_cleanup(...)
  7. │   └─.f(.x[[i]], .y[[i]], ...)
  8. │     └─global function_filtering(.x, .y)
  9. │       └─purrr::map2(features_edgeR[1], features_NOIS, ~.x %>% inner_join(.y))
 10. │         └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
 11. │           ├─purrr:::with_indexed_errors(...)
 12. │           │ └─base::withCallingHandlers(...)
 13. │           ├─purrr:::call_with_cleanup(...)
 14. │           └─.f(.x[[i]], .y[[i]], ...)
 15. │             └─.x %>% inner_join(.y)
 16. ├─dplyr::inner_join(., .y)
 17. ├─dplyr:::inner_join.data.frame(., .y)
 18. │ └─dplyr:::join_mutate(...)
 19. │   └─dplyr:::check_na_matches(na_matches, error_call = error_call)
 20. └─base::.handleSimpleError(...)
 21.   └─purrr (local) h(simpleError(msg, call))
 22.     └─cli::cli_abort(...)
 23.       └─rlang::abort(...)
Execution halted
methornton commented 1 year ago

Here is the output from the run after the pkgconfig() error.

Filtering out low count features...
897 features are to be kept for differential expression analysis with filtering method 1
Filtering out low count features...
1433 features are to be kept for differential expression analysis with filtering method 3
Joining with `by = join_by(value)`
Joining with `by = join_by(value)`
Filtering out low count features...
4054 features are to be kept for differential expression analysis with filtering method 1
Filtering out low count features...
2910 features are to be kept for differential expression analysis with filtering method 3
Joining with `by = join_by(value)`
Joining with `by = join_by(value)`
$salmon
null device 
          1 

$fc
null device 
          1 

Warning messages:
1: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
2: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
3: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
4: In calcNormFactors.DGEList(dgl_fil_data, method = .x) :
  object contains offsets, which take precedence over library
sizes and norm factors (and which will not be recomputed).
$salmon
null device 
          1 

$fc
null device 
          1 

$salmon
pdf 
  2 

$fc
pdf 
  2 

[1] "There is no batch, we will use only the groups"
[1] "There is no batch, we will use only the groups"
$salmon
pdf 
  2 

$fc
pdf 
  2 

Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information. 

Attaching package: ‘XVector’

The following object is masked from ‘package:purrr’:

    compact

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Joining with `by = join_by(sncRNA)`
Error in enc2utf8(path) : argument is not a character vector
Calls: %>% ... mutate -> <Anonymous> -> standardise_path -> as.list
Execution halted
methornton commented 1 year ago

Hi @ConYel

I ran the code snippet that you posted and it does complete. The annot_tbl is GRanges. here is the str.

> str(annot_tbl)
Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 61 levels "chr1","chr2",..: 1 10 11 12 13 14 15 16 17 18 ...
  .. .. ..@ lengths        : int [1:333] 49655 49893 39767 43376 43690 42556 39669 35987 42916 36112 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:888532] 3056358 3056360 3056361 3056758 3056765 3056803 3056803 3056803 3056803 3056803 ...
  .. .. ..@ width          : int [1:888532] 27 25 24 30 28 26 28 29 30 31 ...
  .. .. ..@ NAMES          : NULL
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 2 1 2 1 2 1 2 1 2 1 ...
  .. .. ..@ lengths        : int [1:267841] 5 5 1 1 1 2 1 2 1 5 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. ..@ seqnames   : chr [1:61] "chr1" "chr2" "chr3" "chr4" ...
  .. .. ..@ seqlengths : int [1:61] 195154279 181755017 159745316 156860686 151758149 149588044 144995196 130127694 124359700 130530862 ...
  .. .. ..@ is_circular: logi [1:61] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. ..@ genome     : chr [1:61] "mm39" "mm39" "mm39" "mm39" ...
  ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 888532
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  .. .. ..@ listData       :List of 10
  .. .. .. ..$ source       : Factor w/ 87 levels "ENA,PirBase",..: 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ type         : Factor w/ 1 level "exon": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ score        : num [1:888532] NA NA NA NA NA NA NA NA NA NA ...
  .. .. .. ..$ phase        : int [1:888532] NA NA NA NA NA NA NA NA NA NA ...
  .. .. .. ..$ gene_id      : chr [1:888532] "URS0000253E70_GR_chr1_3056358_3056384_27_-" "URS000042B783_GR_chr1_3056360_3056384_25_-" "URS00004DC026_GR_chr1_3056361_3056384_24_-" "URS0000305867_GR_chr1_3056758_3056787_30_-" ...
  .. .. .. ..$ GENCODE_annot: chr [1:888532] "no_overlap" "no_overlap" "no_overlap" "no_overlap" ...
  .. .. .. ..$ sRNA_id      : chr [1:888532] "URS0000253E70" "URS000042B783" "URS00004DC026" "URS0000305867" ...
  .. .. .. ..$ gene_type    : chr [1:888532] "piRNA" "piRNA" "piRNA" "piRNA" ...
  .. .. .. ..$ seq_RNA      : chr [1:888532] "TGTGACTCTAGAGAACCCTGACTAATA" "TGTGACTCTAGAGAACCCTGACTAA" "TGTGACTCTAGAGAACCCTGACTA" "TGAACTACAATCCAGAATTGGAAGGCTCAC" ...
  .. .. .. ..$ sRNA_id2     : chr [1:888532] "URS0000253E70_GR_chr1_3056358_3056384_27_-" "URS000042B783_GR_chr1_3056360_3056384_25_-" "URS00004DC026_GR_chr1_3056361_3056384_24_-" "URS0000305867_GR_chr1_3056758_3056787_30_-" ...
  ..@ elementType    : chr "ANY"
  ..@ metadata       : list()

It looks like complete_biotypes_seqs is a tibble. Does this look correct?


> head(complete_biotypes_seqs)
# A tibble: 6 × 7
  source      sncRNA            GENCODE_annot sRNA_id gene_type seq_RNA sRNA_id2
  <fct>       <chr>             <chr>         <chr>   <chr>     <chr>   <chr>   
1 ENA,PirBase URS0000253E70_GR… no_overlap    URS000… piRNA     TGTGAC… URS0000…
2 ENA,PirBase URS000042B783_GR… no_overlap    URS000… piRNA     TGTGAC… URS0000…
3 ENA,PirBase URS00004DC026_GR… no_overlap    URS000… piRNA     TGTGAC… URS0000…
4 ENA,PirBase URS0000305867_GR… no_overlap    URS000… piRNA     TGAACT… URS0000…
5 ENA,PirBase URS00003E8F70_GR… no_overlap    URS000… piRNA     TGGAAT… URS0000…
6 ENA,PirBase URS0000193E98_GR… no_overlap    URS000… piRNA     TAGTCA… URS0000…

Here is the output of check.


> comp_FC_sal %>% 
+   bind_rows(.id = "method") %>% 
+   pivot_longer(cols = !c(method,sncRNA)) %>% 
+   pivot_wider(names_from = c(name, method),
+               values_from = value)
# A tibble: 1,277 × 11
   sncRNA      CTR.Control_salmon EXP.Ace_salmon EXP.Lyral_salmon TRN.Ace_salmon
   <chr>                    <dbl>          <dbl>            <dbl>          <dbl>
 1 URS0000690…              340.           245.             339.           653. 
 2 URS000075D…              237.           295.             277.           169. 
 3 URS00006AA…             5532.          5608.            6783.          4832. 
 4 URS0000B34…             1459.          2014.            2051.          1849. 
 5 URS00006FD…              916.          1254.            1660.           596. 
 6 URS000230F…              115.           104.             327.             0  
 7 URS00001FE…               90.7          145.             253.            80.8
 8 URS0000250…             6674.          7384.            6448.          8927. 
 9 URS000079A…               69.7          142.              38.1           81.1
10 URS0000636…               84.5           92.7             96.3          148. 
# ℹ 1,267 more rows
# ℹ 6 more variables: TRN.Lyral_salmon <dbl>, CTR.Control_fc <dbl>,
#   EXP.Ace_fc <dbl>, EXP.Lyral_fc <dbl>, TRN.Ace_fc <dbl>, TRN.Lyral_fc <dbl>
# ℹ Use `print(n = ...)` to see more rows
>

Please let me know id you see anything obvious. Thank you!

ConYel commented 1 year ago

Hello @methornton , could you try run this:

comp_FC_sal <- map2(norm_dgls, list("_salmon", "_fc"), ~function_comp_groups(.x,.y))

annot_tbl <- file.path("human_data","sncRNA_piRNBnk_RNACent_GRCh38_v34.gtf") %>% 
  read_gff2()

complete_biotypes_seqs <- annot_tbl %>% 
  as_tibble() %>% 
  distinct(gene_id, .keep_all = TRUE) %>% 
  select(!c(seqnames:strand,type:phase)) %>% 
  dplyr::rename("sncRNA" = gene_id)

salmon_FC_cpm_union_grouped <- comp_FC_sal %>% 
  bind_rows(.id = "method") %>% 
  pivot_longer(cols = !c(method,sncRNA)) %>% 
  pivot_wider(names_from = c(name, method),
              values_from = value) %>% 
  left_join(complete_biotypes_seqs) %>%
  dplyr::select(sncRNA, gene_type, everything())

  salmon_FC_cpm_union_grouped %>% 
  write_tsv(file.path(dirname(dat_path[1]), "salmon_FC_cpm_union_grouped.txt"))

Let me know if this exports the results to the txt file.