EdgeR output for miRNA analysis

[Dario Veneziano]

Hello,

I've just finished running for the first time miARma on a set of sRNAseq data files for known miRNA analysis and everything ended without error. Nonetheless, the final results .xls file generated by ED_EdgeR.R containing the differentially expressed information does not contain the first column which should list the miRNAs (there are just 4 columns instead of 5: logFC, logCMP, PValue and FDR). I'm running miARma on Ubuntu 16.04LTS.

Can you help me with this issue?

Thanks!

[Eduardo Andres Leon]

Dear Dario, Thank you very much for using miARma !!. Another user reported the same error than you. We are investigating the problem, and, at the moment we think that edgeR or limma have modified their output.

Could you tell me which versions are you running for: R bioconductor edgeR and limma ?

kind regards

[Dario Veneziano]

Dear Eduardo, Thank you for your prompt response!

So, I'm running R 3.2.3, EdgeR 3.12.1 and limma 3.26.9

Which versions of these components is miARma currently compatible with?

[Eduardo Andres Leon]

Dear Dario, miARma was developed using :

sessionInfo() R version 3.3.1 (2016-06-21)

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

other attached packages: [1] edgeR_3.14.0 limma_3.28.21 BiocInstaller_1.22.3

Could you try to update your setup ? This could be a great help in order to find a permanent solution

Thanks in advance

[Dario Veneziano]

Dear Edoardo,

I have updated the system as you suggested and this is the session info:

sessionInfo() R version 3.3.2 (2016-10-31) 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
[4] 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
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] RCurl_1.95-4.8 bitops_1.0-6 NOISeq_2.16.0
[4] Matrix_1.2-8 Biobase_2.32.0 BiocGenerics_0.18.0 [7] genefilter_1.54.2 edgeR_3.14.0 limma_3.28.21
[10] BiocInstaller_1.22.3

loaded via a namespace (and not attached): [1] Rcpp_0.12.9 AnnotationDbi_1.34.4 IRanges_2.6.1
[4] xtable_1.8-2 lattice_0.20-34 tools_3.3.2
[7] grid_3.3.2 DBI_0.5-1 survival_2.40-1
[10] digest_0.6.12 S4Vectors_0.10.3 memoise_1.0.0
[13] RSQLite_1.1-2 stats4_3.3.2 XML_3.98-1.5
[16] annotate_1.50.1

I tried re-running miARma on the same data but I ended up with the same problem: the first column in edgeR results is missing (basically, there are no miRNA names!).

[Eduardo Andres Leon]

ummmm that sounds really strange ....

Could be possible to have your target.txt, contrast.txt, ReadCount_results folder and your ini file ? I'd like to reproduce your error

Edu

[Dario Veneziano]

Sure, send me your email and I'll attach the files you requested.