TMM normalized CPM

Question

[maryak]

I found Differently expressed genes using EdgeR during the process the raw count are converted into TMM normalized CPM. Once i get differently expressed genes can i use TPM values instead of CPM for further machine learning classification.

[ATpoint]

Look, these sorts of questions cannot really be answered. If you classifier works wenn with TPM then use it. If not, use whatever the authors of it recommend. In the end, you write what you did in the methods and that's it. There are many ways to run an analysis. It's fine unless obviously wrong.