Problem running the EdgeR analysis on miARma
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
Comments (7)
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Hi Eduardo,
Thank you for your input. I will give this a shot to see if it works.
Thanks, Sid
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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
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Hi Shuklasidd, Could you send me your logs files (miARma_log and miARma_stat ?)
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Hi Eduardo,
Attached are the stat and log file for this run.
Thanks, Sid
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I don't see any attached file
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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