Dear Gordan,
I am writing to get your feedback on using normalized count as an input to edgeR algorithm. I understand that edgeR expects raw counts as input, and I wondered if there is a workaround in the pipeline to use normalized counts instead. Can you please advice.
Thanks Shar
Yes, you can use limma-trend to analyse logCPM values, but batch corrected data is another consideration. Generally speaking, batch correction should be done as part of the limma or edgeR linear models. It is not correct to do ComBat batch correction and then pass the results to limma as if they were not corrected.
It is surprising that you would have TMM normalized cpm values but not the original counts.
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What do you mean exactly by a "normalized count"? See for example https://www.biostars.org/p/112637/
Hi Gordon, Thank you for the reply. By normalized count, I mean TMM normalized matrix using CPM or an output from ComBat or removeBatchEffect with batch or covariate(s) adjustment. Appreciate your feedback. Thanks Shar
Sorry, got posted twice..