known miRNA pipeline using edgeR for DE

[Former user]

-bash-4.1$ perl miARma Examples/basic_examples/miRNAs/Known_miRNAs/5.DEAnalysis/5.1.DEAnalysis_EdgeR_miRNAs.ini

miARma, miRNA and RNASeq Multiprocess Analysis

miARma v 1.6.1 (Feb-2017)

Created at Computational Biology and Bioinformatics Group (CbBio)

Institute of Biomedicine of Seville. IBIS (Spain)

Copyright (c) 2017 IBIS. All rights reserved.

mail : [e-mail]

[Tue Feb 28 10:55:34 2017] Starting a miARma analysis for miRNA [Tue Feb 28 10:55:34 2017] Checking provided parameters for: DEAnalysis. [Tue Feb 28 10:55:34 2017] Checking General-output_dir parameter ... Exists! [Tue Feb 28 10:55:34 2017] The folder specified in (output_dir=Examples/basic_examples/miRNAs/Known_miRNAs/results/) already exists. [Tue Feb 28 10:55:34 2017] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Tue Feb 28 10:55:40 2017] Continue. [Tue Feb 28 10:55:40 2017] All parameters are correct. [Tue Feb 28 10:55:40 2017] Starting a differential expression analysis using EdgeR software(s) QC_EdgeR :: [Tue Feb 28 10:55:40 2017] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/mnt/ris-fas1a/linux_users2/gossnera/build/cbbio-miarma-ba7e51dd6d2e/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/mnt/ris-fas1a/linux_users2/gossnera/build/cbbio-miarma-ba7e51dd6d2e/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/mnt/ris-fas1a/linux_users2/gossnera/build/cbbio-miarma-ba7e51dd6d2e/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="cut_bw1-ReadCount.tab", targetfile="/mnt/ris-fas1a/linux_users2/gossnera/build/cbbio-miarma-ba7e51dd6d2e/Examples/basic_examples/miRNAs/data/targets.txt", label="ParaTB_cut_bw1", filter="yes", cpmvalue=2, repthreshold=1, normethod="TMM")

Problem while running this R command: print(resultsfiles)

Error: print(resultsfiles) : object 'resultsfiles' not found Execution halted

get the following error when trying to use the differential expression module as part of pipeline or lone module? Have also readcount problem when using pipeline as used BWA aligner have to rename the results folder with BWA alignments to Bowtie1_results before ReadCount module will use alignments.

[Eduardo Andres Leon]

Dear user, This problem is usually related with the names used as header in the tab file (cut_bw1-ReadCount.tab) and the names in the target.txt file. They must be the same

Let me know

[A Gossner]

Thank you for your prompt reply. Have two directories from readcount output, Readcount_results containing two files "-ReadCount.tab" and "-Size.tab", the other directory -readcount_results containing .tab and .tab.summary files eg. 934N0019_cut_merged_bwa.tab Have used filename 934N0019 in targets.txt file, is this correct?

[Eduardo Andres Leon]

So may be this is the problem.

As I see in your first mail, the tab file must named: file="cut_bw1-ReadCount.tab"

[A Gossner]

okay so renamed file "results/Readcount_results/-ReadCount.tab" to "results/Readcount_results/cut_bw1-ReadCount.tab" but same error again?

[Eduardo Andres Leon]

Could you send me the tab file + the ini file + target.txt + contrast.txt + 2 log files ?

I’ll try to reproduce your error

Thanks a lot

[A Gossner]

emailed files. Thank you.

[A Gossner]

Solved the problem for me hope this will help others. Even when running either of the miRNA examples known or denovo always stopped at differential expression module with error about R. Two different linux builds later and loading R and Bioconductor more times than i care to remember all works perfectly when run the miARma perl script is run as sudo.

[Eduardo Andres Leon]

Interesting … I used your files and I had no problem …. But nevertheless I never thought it was related with Bioconductor Although it is true that I always recommend (only for users with a previous bioconducotor version), to re-install all packages and select yes (that is really important), when bioconductor asks to create a personal library folder.

You can enter in lib/Perl/CbBio/RNASeq/R-Scripts and source (from a r session) the QC_EdgeR.R file. This should install all your packages. If this fails, your previous bioconductor installation is wrong

Edu