Trinity error using Perl script

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4.9 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

Trinity Perl script • 1.3k views

ADD COMMENT • link updated 4.9 years ago by ATpoint 81k • written 4.9 years ago by singh.bioinfo ▴ 30

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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

ADD REPLY • link 4.9 years ago by lieven.sterck 15k

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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.

ADD REPLY • link 4.9 years ago by ATpoint 81k

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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?

ADD REPLY • link 4.9 years ago by GenoMax 141k

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