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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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Need help with makeModels() testvar error #41

Closed fruce-ki closed 5 years ago

fruce-ki commented 6 years ago

I'm trying to run the F-statistic version of derfinder. I follow the example in the docs, with only difference that my fullcov equivalent has five chromosomes instead of just one, and only two samples instead of a dozen. I've reached a dead end at attempting to make the models.

cv <- c("fpa7", "wt") 
sampleDepths <- sampleDepth(collapseFullCoverage(allcov), 1)
sampleDepths

## fpa7-1.100%  wt2-1.100% 
##   24.53941    24.42730 

demodels <- makeModels(sampleDepths, testvars=cv, adjustvars=NULL)
Error in makeModels(sampleDepths, testvars = cv, adjustvars = ifelse(length(cf) ==  : 
  The length of 'testvars' and the number of sample library size adjustments do not match.

The length of my testvars is equal to the number of columns I got out of sampleDepth(), and equal to the number of columns in each of the chromosome coverage tables in allcov. From what I understand from the user guide example, testvar is the category value of each sample. Two samples, two values. The function documentation makes reference to columns in a coverageInfo$coverage but there is no such variable in my session or in the user manual example, and there is no indication where to find it. So from the available documentation and examples I cannot figure out what I'm doing wrong.

fruce-ki commented 6 years ago 
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] derfinderData_0.112.0 BiocInstaller_1.28.0  derfinder_1.12.6      rtracklayer_1.38.3    GenomicRanges_1.30.3  GenomeInfoDb_1.14.0  
 [7] IRanges_2.12.0        S4Vectors_0.16.0      BiocGenerics_0.24.0   data.table_1.10.4-3  

loaded via a namespace (and not attached):
 [1] Biobase_2.38.0             httr_1.3.1                 RMySQL_0.10.14             bit64_0.9-7                splines_3.4.1             
 [6] foreach_1.4.4              GenomicFiles_1.14.0        Formula_1.2-2              bumphunter_1.20.0          assertthat_0.2.0          
[11] latticeExtra_0.6-28        doRNG_1.6.6                blob_1.1.1                 BSgenome_1.46.0            GenomeInfoDbData_1.0.0    
[16] Rsamtools_1.30.0           progress_1.1.2             pillar_1.2.1               RSQLite_2.1.0              backports_1.1.2           
[21] lattice_0.20-35            digest_0.6.15              RColorBrewer_1.1-2         XVector_0.18.0             checkmate_1.8.5           
[26] qvalue_2.10.0              colorspace_1.3-2           htmltools_0.3.6            Matrix_1.2-14              plyr_1.8.4                
[31] XML_3.98-1.10              biomaRt_2.34.2             zlibbioc_1.24.0            xtable_1.8-2               scales_0.5.0              
[36] BiocParallel_1.12.0        tibble_1.4.2               htmlTable_1.11.2           pkgmaker_0.22              ggplot2_2.2.1             
[41] SummarizedExperiment_1.8.1 GenomicFeatures_1.30.3     nnet_7.3-12                lazyeval_0.2.1             survival_2.41-3           
[46] magrittr_1.5               memoise_1.1.0              foreign_0.8-69             registry_0.5               tools_3.4.1               
[51] prettyunits_1.0.2          matrixStats_0.53.1         stringr_1.3.0              locfit_1.5-9.1             munsell_0.4.3             
[56] rngtools_1.2.4             cluster_2.0.7-1            DelayedArray_0.4.1         AnnotationDbi_1.40.0       Biostrings_2.46.0         
[61] compiler_3.4.1             rlang_0.2.0                grid_3.4.1                 RCurl_1.95-4.10            iterators_1.0.9           
[66] rstudioapi_0.7             VariantAnnotation_1.24.5   htmlwidgets_1.0            bitops_1.0-6               base64enc_0.1-3           
[71] derfinderHelper_1.12.0     codetools_0.2-15           gtable_0.2.0               DBI_0.8                    reshape2_1.4.3            
[76] R6_2.2.2                   GenomicAlignments_1.14.2   gridExtra_2.3              knitr_1.20                 bit_1.1-12                
[81] Hmisc_4.1-1                stringi_1.1.7              Rcpp_0.12.16               rpart_4.1-13               acepack_1.4.1
andrewejaffe commented 6 years ago

You can't calculate an f statistic with only two samples

A

On Tue, Apr 10, 2018, 12:35 PM Dr. Kimon Froussios notifications@github.com wrote:

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] derfinderData_0.112.0 BiocInstaller_1.28.0 derfinder_1.12.6 rtracklayer_1.38.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 [7] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 data.table_1.10.4-3

loaded via a namespace (and not attached): [1] Biobase_2.38.0 httr_1.3.1 RMySQL_0.10.14 bit64_0.9-7 splines_3.4.1 [6] foreach_1.4.4 GenomicFiles_1.14.0 Formula_1.2-2 bumphunter_1.20.0 assertthat_0.2.0 [11] latticeExtra_0.6-28 doRNG_1.6.6 blob_1.1.1 BSgenome_1.46.0 GenomeInfoDbData_1.0.0 [16] Rsamtools_1.30.0 progress_1.1.2 pillar_1.2.1 RSQLite_2.1.0 backports_1.1.2 [21] lattice_0.20-35 digest_0.6.15 RColorBrewer_1.1-2 XVector_0.18.0 checkmate_1.8.5 [26] qvalue_2.10.0 colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-14 plyr_1.8.4 [31] XML_3.98-1.10 biomaRt_2.34.2 zlibbioc_1.24.0 xtable_1.8-2 scales_0.5.0 [36] BiocParallel_1.12.0 tibble_1.4.2 htmlTable_1.11.2 pkgmaker_0.22 ggplot2_2.2.1 [41] SummarizedExperiment_1.8.1 GenomicFeatures_1.30.3 nnet_7.3-12 lazyeval_0.2.1 survival_2.41-3 [46] magrittr_1.5 memoise_1.1.0 foreign_0.8-69 registry_0.5 tools_3.4.1 [51] prettyunits_1.0.2 matrixStats_0.53.1 stringr_1.3.0 locfit_1.5-9.1 munsell_0.4.3 [56] rngtools_1.2.4 cluster_2.0.7-1 DelayedArray_0.4.1 AnnotationDbi_1.40.0 Biostrings_2.46.0 [61] compiler_3.4.1 rlang_0.2.0 grid_3.4.1 RCurl_1.95-4.10 iterators_1.0.9 [66] rstudioapi_0.7 VariantAnnotation_1.24.5 htmlwidgets_1.0 bitops_1.0-6 base64enc_0.1-3 [71] derfinderHelper_1.12.0 codetools_0.2-15 gtable_0.2.0 DBI_0.8 reshape2_1.4.3 [76] R6_2.2.2 GenomicAlignments_1.14.2 gridExtra_2.3 knitr_1.20 bit_1.1-12 [81] Hmisc_4.1-1 stringi_1.1.7 Rcpp_0.12.16 rpart_4.1-13 acepack_1.4.1

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fruce-ki commented 6 years ago

Oh. Fair enough. I normally would have more than 2 samples indeed. Is that what's causing this error or can there be other things going on as well? This cause is certainly not reflected in the message.

Thanks!

lcolladotor commented 6 years ago

Hi,

If you want more feedback, please give us a toy example or subset/anonymized version of your data and the full code that reproduces the error (like creating allcov). Use a few more samples too so we can rule that being a part of the issue.

Best, Leonardo

lcolladotor commented 5 years ago

Hi @fruce-ki, should we close this issue?

fruce-ki commented 5 years ago

Yes, go ahead. I have no idea anymore what it was about anyway.

On 20 Sep 2019 16:25, Leonardo Collado-Torres notifications@github.com wrote:

Hi @fruce-kihttps://github.com/fruce-ki, should we close this issue?

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lcolladotor commented 5 years ago

Ok! If you need help with another issue please let us know. Best, Leo