This is a test version of Biostars. For the public version, visit https://www.biostars.org.
error in introducing different batches to DeSeq2

Dear all,

I faced with a problem in introducing different batches to DeSeq2.

I have chemotherapy resistant ans sensitive samples that include 3 different cell line (1,2,3) and have been performed by 3 different illumina sequencer (HiSeq 2500, HiSeq 3000 and next seq).

I got the htseq counts files of all samples. However when I want to introduce these three batches (factor 1: Resistant-sensitive, factor 2: cell line (A,B,C) and factor 3: the version of instrument (2500,3000 and next seq) to DeSeq2 in Galaxy, I get the error message that there are some thing wrong with your inputs.

I would appreciate any advice

Nazanin

rna-seq deseq2 introducing batches
• 632 views • link
written by nazaninhoseinkhan nazaninhoseinkhan

Dear all, I repeat the factor introduction steps and my problem was solved. Happy new year 2019 to all Galaxy members. I wish you all health, wealth and peace in 2019. Nazanin

• 0 views • link
written by nazaninhoseinkhan nazaninhoseinkhan

Hi Nazanin,

How did you account the batch effects from three different sequencers? I have also used 2 different sequencers (Hiseq 4000 and Novaseq) for my treatment and control samples of two different genotypes.

Thanks

• 0 views • link
written by rthapa • rthapa

Hello nazaninhoseinkhan!

OP solved issue.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this