How could i use Quantile (or) TMM normalized counts as input for DESEQ2?

Question

[k.kathirvel93]

Hi EveryOne,

How could i use Quantile (or) TMM normalized counts as input for DESEQ2? ..........Thanks advance........

Answer 1

[WouterDeCoster]

You should not.

DESeq2 expects raw counts, not normalised by any means. Try to get access to the original data.

Answer 2

[ATpoint]

Hi k.kathirvel93,

please spend some quality time on the outstandingly extensive DESeq2 manual, which also contains a section about the expected input reads. As Wouter already mentioned, it is raw counts.

It is important to provide count matrices as input for DESeq2’s statistical model (Love, Huber, and Anders 2014) to hold, as only the count values allow assessing the measurement precision correctly. The DESeq2 model internally corrects for library size, so transformed or normalized values such as counts scaled by library size should not be used as input.