RNAseq Analysis using RUVs

Question

[manish20072013]

I have three groups each have 4 replicates. The conditions for each group were same before preparing library and then sequencing. Now I have to analyse the read counts to find DE genes between Group1 vs Group2, Group2 vs Group3 and Group1 vs Group3.

But I do not know whether to combine all the groups in one file then perform RUVs normalization and find DE genes in each case OR make a separate file for each case, then perform RUVs normalization separately on each file and then find the DE genes in each case.

Thanks!

[Kristoffer Vitting-Seerup]

I'm not sure what your question is. Are you asking about RUV normalization before DE analysis of the groups or are you asking about normalization for another DE analysis? In the later case could you elaborate on what that is?

[GouthamAtla]

You can perform normalization using a single matrix comprised of all the samples. Then after normalization, perform differential analysis according to groups of your interest.