Question: Regarding error in Trinity edgeR calculation
0
gravatar for sakshi.rajput55
10 weeks ago by
sakshi.rajput550 wrote:

Hello all,

I am working on Trinity for denovo assembly of my data but stuck at differential gene expression step(screenshot). I have 3 sample files and followed the steps as mentioned in the trinity tutorial but somehow getting this error in edgeR.

Error, cmd: R --vanilla -q < matrix.counts.matrix.align_estimate_rsem_P3_vs_align_estimate_rsem_unP3.align_estimate_rsem_unP3.vs.align_estimate_rsem_unP3. EdgeR.Rscript died with ret (32512) at /app/setup/trinityrnaseq-2.2.0/analysis/diffenetialexpression/run_DE_analysis.pl     line 712.

WARNING: This EdgeR comparison failed...

Plz, guide me.

Best Regards, Sakshi

edger • 75 views
ADD COMMENTlink modified 10 weeks ago by Gordon Smyth37k • written 10 weeks ago by sakshi.rajput550
Answer: Regarding error in edgeR calculation
1
gravatar for James W. MacDonald
10 weeks ago by
United States
James W. MacDonald50k wrote:

You are using a Perl script that the Trinity author created, which just happens to call some functions in edgeR, so your question really has to do with that Perl script rather than edgeR. Rather than asking here, you should be asking the authors of Trinity on their Google Groups page.

ADD COMMENTlink written 10 weeks ago by James W. MacDonald50k

Thanks a lot, James!

ADD REPLYlink written 10 weeks ago by sakshi.rajput550
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