Problem running the EdgeR analysis on miARma

[Former user]

Hello,

I am trying to align some processed reads to miRbase and get DE analysis using miARma. I keep getting this problem once the program gets to the DEanalysis step.

As an aside, I am running miARma on our computing cluster, so there are certain limitations with the directories I can access or have permission to edit.

[Fri May 19 21:57:39 2017] Starting a differential expression analysis using EdgeR software(s) Problem while running this R command: setwd("/data/results/Readcount_results") source("http://valkyrie.us.es/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") resultsfiles<-QC_EdgeR(projectdir="/data/results",dir="/data/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/data/gtf/targetsPARN.txt", label="PARNKD_nat_bw1", filter="yes")

Error: file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : unable to resolve 'valkyrie.us.es' Execution halted

[Eduardo Andres Leon]

Dear user, First of all, I recommend you to download the latest version (https://bitbucket.org/cbbio/miarma/get/master.tar.bz2), where there is no need to connect to valkyrie.

Although you need to install biocondcutor and several R packages such as "ggplot2", "Rcpp","edgeR","NOISeq","gplots","lattice","genefilter","RColorBrewer".

Regards

[Shuklasidd]

Hi Eduardo,

Thank you for your input. I will give this a shot to see if it works.

Thanks, Sid

[Shuklasidd]

Hi Eduardo,

I tried the latest version of miARma-seq. It seems to have resolved the valkyrie issue. However, I am getting a different kind of error at the DE analysis step:

Starting a differential expression analysis using EdgeR software(s) Problem while running this R command: print(resultsfiles)

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

Any help regarding how to resolve this would be much appreciated.

Thanks, Sid

[Eduardo Andres Leon]

Hi Shuklasidd, Could you send me your logs files (miARma_log and miARma_stat ?)

[Shuklasidd]

Hi Eduardo,

Attached are the stat and log file for this run.

Thanks, Sid

[Eduardo Andres Leon]

I don't see any attached file