Error: plot.window(xlim, ylim, log = log, ...) :

[Rupinder Kaur]

Hello SIr, I try to run miARma using this configuration file(conf.ini) and got an error.

[Rupinder Kaur]

Hello Sir, The previous issue is resolved. Now i tried to run the file and again got an error

**Problem while running this R command: print(resultsfiles)

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

As you said earlier I run the following commands

bash$>cd /home/rupinder/NGS/cbbio-miarma-42e187a7f514 bash$>R R>source("/home/rupinder/NGS/cbbio-miarma-42e187a7f514/lib/CbBio/RNASeq/R-Scripts/DE_EdgeR.R") R>setwd("/home/rupinder/NGS/results/Readcount_results") R> DE_EdgeR(projectdir="/home/rupinder/NGS/results/EdgeR_results",dir="/home/rupinder/NGS/results/Readcount_results", file="/home/rupinder/NGS/results/Readcount_results/cut_bw1-ReadCount.tab", targetfile="/home/rupinder/NGS/cbbio-miarma-42e187a7f514/target.txt", label="OSCC_cut_bw1", contrastfile="/home/rupinder/NGS/cbbio-miarma-42e187a7f514/contrast.txt", filter="yes", rpkm="yes", file_size="/home/rupinder/NGS/results/Readcount_results/cut_bw1-Size.tab", cpm="yes")

and got an error DE_EdgeR(projectdir="/home/rupinder/NGS/results/EdgeR_results",dir="/home/rupinder/NGS/results/Readcount_results", file="/home/rupinder/NGS/results/Readcount_results/cut_bw1-ReadCount.tab", targetfile="/home/rupinder/NGS/cbbio-miarma-42e187a7f514/target.txt", label="OSCC_cut_bw1", contrastfile="/home/rupinder/NGS/cbbio-miarma-42e187a7f514/contrast.txt", filter="yes", rpkm="yes", file_size="/home/rupinder/NGS/results/Readcount_results/cut_bw1-Size.tab", cpm="yes") 2018-06-29 13:01:15 Starting Differential expression analysis with EdgeR of OSCC_cut_bw1 Error in setwd(workingDir) : cannot change working directory Again, need help ! Thank you

[Eduardo Andres Leon]

Dear Rupy,

First of all, could you rename the miARma folder ? It can help me to identify the error, So in the terminal you have to type:

bash$> mv /home/rupinder/NGS/cbbio-miarma-42e187a7f514 /home/rupinder/NGS/miARma

Then pleease, run the whole pipeline and send the the log and stat files (miARma_log_xx and miARma_stat_xx).

And please try not to mix issues because it is difficult to follow all bugss. So as the issue in the title is resolved, I'll close it, so please create a new one f you have a new problem

E