IsomirDataSeqFromFiles error

[hmkim]

> obj <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
Error in initialize(value, ...) : 
  cannot use object of class “SummarizedExperiment0” in new():  class “IsomirDataSeq” does not extend that class

Hi, Ipantano

Would you give me any suggestion about this error ?

[lpantano]

hum, can you send me the sessionInfo() output? I think is a problem of version. Did you install the package recently?

sent not from my computer

On Apr 28, 2016, at 00:28, Hyunmin notifications@github.com wrote:

obj <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T) Error in initialize(value, ...) : cannot use object of class “SummarizedExperiment0” in new(): class “IsomirDataSeq” does not extend that class Hi, Ipantano

Would you give me any suggestion about this error ?

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[lpantano]

can you check to install again this package from github origin/master. I think is a problem with summarixedexperiment object and maybe I fixed it.

thanks

[hmkim]

Ok. I'll try to run again and report it.

Thanks.

[hmkim]

Sorry for delaying of my reply.

I solve the before problem.

I have another issue about this function in Isomir.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = TRUE)

> design
     type batch phenotype
PK_1   PK  None        PK
PI_1   PI  None        PI
PI_2   PI  None        PI
SI_1   SI  None        SI
SI_2   SI  None        SI
SK_1   SK  None        SK

> files[rownames(design)]
                                                               PK_1 
"/Users/brandon/Downloads/work/upload/PK_1/PK_1-novel-ready.counts" 
                                                               PI_1 
"/Users/brandon/Downloads/work/upload/PI_1/PI_1-novel-ready.counts" 
                                                               PI_2 
"/Users/brandon/Downloads/work/upload/PI_2/PI_2-novel-ready.counts" 
                                                               SI_1 
"/Users/brandon/Downloads/work/upload/SI_1/SI_1-novel-ready.counts" 
                                                               SI_2 
"/Users/brandon/Downloads/work/upload/SI_2/SI_2-novel-ready.counts" 
                                                               SK_1 
"/Users/brandon/Downloads/work/upload/SK_1/SK_1-novel-ready.counts" 

Can you check this error?

[lpantano]

Hi,

what is the error you are getting?

sent not from my computer

On May 25, 2016, at 03:08, Hyunmin notifications@github.com wrote:

Sorry for delaying my reply.

I solve the before problem.

I have another issue about this function in Isomir.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = TRUE)

design type batch phenotype PK_1 PK None PK PI_1 PI None PI PI_2 PI None PI SI_1 SI None SI SI_2 SI None SI SK_1 SK None SK files[rownames(design)] PK_1 "/Users/brandon/Downloads/work/upload/PK_1/PK_1-novel-ready.counts" PI_1 "/Users/brandon/Downloads/work/upload/PI_1/PI_1-novel-ready.counts" PI_2 "/Users/brandon/Downloads/work/upload/PI_2/PI_2-novel-ready.counts" SI_1 "/Users/brandon/Downloads/work/upload/SI_1/SI_1-novel-ready.counts" SI_2 "/Users/brandon/Downloads/work/upload/SI_2/SI_2-novel-ready.counts" SK_1 "/Users/brandon/Downloads/work/upload/SK_1/SK_1-novel-ready.counts" Can you check this error?

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[hmkim]

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T) Error in if (row["subs"] == "0") return(c(.seq, row["subs"])) else if (sum(tab.fil$subs == : missing value where TRUE/FALSE needed

I think this error come up with my data. Can you check this ?

[lpantano]

Can you check this code to isolate what file is giving the error:

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)

Also, can you paste the few lines of some of the file is reading, just in case there is something obvious.

[hmkim]

> obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)
Error: object 'False' not found

novel miRNA by mirdeep2

total miRNA expression

files = mirdeep2_files

names(files) = sapply(files, function(x){
  gsub("-novel-ready.counts", "", basename(x))
})

#obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)

If you want to any data related to this problem, please tell me about that.

Thanks!

[lpantano]

sorry, it should be FALSE

let me know the output. Then if we get one file is failing maybe you can sending me file to my email.

thanks

sent not from my computer

On May 29, 2016, at 22:28, Hyunmin notifications@github.com wrote:

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False) Error: object 'False' not found

novel miRNA by mirdeep2

total miRNA expression

files = mirdeep2_files

names(files) = sapply(files, function(x){ gsub("-novel-ready.counts", "", basename(x)) })

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False) If you want to any data related to this problem, please tell me about that.

Thanks!

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[hmkim]

I might find the cause of problem.

If some samples don't have the novel miRNA, it is badly for IsomirDataSeqFromFiles.

[design2] have only SI_1, SI_2 and SK_1 sample.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design2)], design = design2 , header = T)

[simonas-j]

Hi Ipantano,

I'm getting the same error and I have no clue what could cause it. See the code below:

head(metafile, n=2) Condition D1416 GIST D1417 GISTaj

head(files.list, n=2) D1416 "/home/simonas/Results/isomir_D1416.mirna" D1417 "/home/simonas/Results/isomir_D1417.mirna"

ids <- IsomirDataSeqFromFiles(files.list, design=metafile, header = TRUE, quiet= FALSE) reading file: /home/simonas/Results/isomir_D1416.mirna Error in if (row["subs"] == "0") return(c(.seq, row["subs"])) else if (sum(tab.fil$subs == : missing value where TRUE/FALSE needed In addition: Warning message: In .put_header(table) : NAs introduced by coercion

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] stringr_1.1.0 isomiRs_1.1.5 SummarizedExperiment_1.2.3 Biobase_2.32.0 GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[7] IRanges_2.6.1 S4Vectors_0.10.3 BiocGenerics_0.18.0 DiscriMiner_0.1-29

loaded via a namespace (and not attached): [1] genefilter_1.54.2 gtools_3.5.0 locfit_1.5-9.1 splines_3.3.1 lattice_0.20-34 colorspace_1.2-7 chron_2.3-47 survival_2.39-5
[9] XML_3.98-1.4 foreign_0.8-67 DBI_0.5-1 BiocParallel_1.6.6 RColorBrewer_1.1-2 plyr_1.8.4 zlibbioc_1.18.0 munsell_0.4.3
[17] gtable_0.2.0 caTools_1.17.1 DESeq2_1.12.4 latticeExtra_0.6-28 GGally_1.2.0 geneplotter_1.50.0 AnnotationDbi_1.34.4 Rcpp_0.12.7
[25] KernSmooth_2.23-15 acepack_1.3-3.3 xtable_1.8-2 readr_1.0.0 scales_0.4.0 gdata_2.17.0 Hmisc_3.17-4 annotate_1.50.1
[33] XVector_0.12.1 gplots_3.0.1 gridExtra_2.2.1 ggplot2_2.1.0 stringi_1.1.2 dplyr_0.5.0 grid_3.3.1 tools_3.3.1
[41] bitops_1.0-6 magrittr_1.5 lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.5
[49] tidyr_0.6.0 Matrix_1.2-7.1 data.table_1.9.6 assertthat_0.1 reshape_0.8.5 R6_2.2.0 rpart_4.1-10 nnet_7.3-12

Thank you in advance!

[lpantano]

Hi,

sorry about this.

can you send me one of the files so I can make sure is not a problem of isomiRs version. You can try to install to last version of the package but I think 1.1.5 was the one that fixed this error.

thanks!

On Oct 20, 2016, at 3:51 AM, simonas-j notifications@github.com wrote:

isomiRs_1.1.5

[simonas-j]

Sorry, for disturbing you. I fixed the problem. I didn't have frequencies in miraligner's .mirna file which caused the problem.

[lpantano]

Let me know if you have more issues in the future