Question: RNAseq Analysis using RUVs
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gravatar for manish20072013
3.1 years ago by
manish2007201310 wrote:

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!

rna-seq next-gen ruvs R • 875 views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.1 years ago by manish2007201310

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?

ADD REPLYlink written 3.0 years ago by kristoffer.vittingseerup3.4k

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.

ADD REPLYlink written 3.0 years ago by geek_y11k
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