Entering edit mode
5.6 years ago
singh.bioinfo
▴
30
Hello all,
I am working on Trinity
for de-novo 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
Hi, apparently your image (screenshot) is not coming through.
For help in adding images to posts have a look here: How to add images to a Biostars post
Your code does not allow any reproduction of the error. Where did you get the script from? If custom-made, please share it. Otherwise it is impossible to help.
That script is part of
trinity
distribution.@sakshi: What do you mean by you have 3 sample files? You just have three samples that you are trying to do DE analysis on?