Deseq2 Etc. Unequal Sample Sizes

Question

[Phil S.]

Hi there,

I got an RNA-seq experiment where I have 8 control and 16 case samples sequenced. Can I use DESeq2 and/or similar tools to discover DE genes without further accounting for the different group sizes(case dbl as large as control) or do I have to account for this somehow? If so, what can/should I do?

Thanks in advance,

Phil

[Teresa]

Hi Devon,

I am facing the same problem. I have 10 control and 48 case samples. I have used all the samples for the analysis with DESEQ2 but I obtain aprox. 3000 DE genes. I think that this high number is because of the unequal sample size. How can I deal with this situation? Is there a way to "correct" by this?

Thanks you a lot,

Teresa

[Devon Ryan]

Please don't resurrect 5 year old threads, instead post things like this as a new question.

With 58 total samples you have quite a bit of power, so if you need a smaller list of genes for further analysis then start filtering by fold-change.

Answer 1

[Devon Ryan]

You can use things as are.