Number of replicates in each group in RNA seq

Question

[dolphiness]

Hi all,

In RNA seq expression analysis, should the number of replicates per group be roughly the same?

In my data I have 2 variables : status (A or B) and phenotype (case or control), but in the number of replicates per each subgroup is very different (e.g 25, 32, 30, 167). Should I sample from each one to get a fixed number of replicates?

Thanks!

[h.mon]

It probably depends on which tool you will use for analysis, but for several tools it doesn't matter. See an answer (and several links) here:

edgeR - DE with one disease sample vs. multiple control samples?

Answer 1

[mark.ziemann]

The statistical packages like DESeq2 should be able to manage with unbalanced replicate numbers as long as the numbers are not too low. Downsampling shouldn't be required. If you still have a doubt, you can ask on the Bioconductor forum [1] tagging the tool that you are using.

1. https://support.bioconductor.org/