This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DEGs with uninsteresed sample files

Hi all,

I am working on some bulkRNAseq data from GEO and my sample description looks like this. I am interested in A vs B, A vs C and B vs C but I am not interested in sample D.

My question is whether I should include sample D for edgeR or DESeq2 to help them estimate some parameters such as commona variance or something. I have learnt about linear regression so I think I should include sample D(that's what the class taught me - reducing SE) but I am not 100% sure that it applies to DEGs.

enter image description here

design bulkrnaseq deg matrix
• 1,513 views • link
updated by swbarnes2 swbarnes2 • written by jkim • jkim

1 answer

If the D samples don't have batch issues, and a PCA shows that they aren't way different from other others, or have way higher variability than the others, you should leave them in.

• 0 views • link
written by swbarnes2 swbarnes2

Thank you for your suggestion. Yes, looking at a PCA plot will help for sure. Do you mind me asking a question? I would like to know what your reasoning about leaving them in is

• 0 views • link
written by jkim • jkim

Log in to answer this question.

More posts like this