Hi guys, I have a simple question. I have RNA-Seq data from different batches. As suggested looking at many posts on-line I have pre-normalized my data (using the TMM from edgeR) then I have corrected them using Combat and then I have re-normalized them (for the library-size) using DESeq2. My question is: is it correct the second normalisation after Combat? Or at least is it not dramatically not-correct? 


Thank you in advance

Best 

Hey,

Sorry, this is ***not*** recommended (by me, and others):

> then I have corrected them using Combat

The way in which you have implemented this batch-correction procedure is neither ideal, irrespective of the use of ComBat, due to the fact that you are normalising your data twice, and by 2 different programs.

Could you please read a recent answer that I gave, here: https://support.bioconductor.org/p/133222/#133225

Kevin