Are original CPMs modified after a batch correction with ComBat-seq?
(CPMs are re-calculated after the process)
Please upvote and/or accept answers rather than adding titles like "closed" which have no meaning. Thank you.
Most likely, yes. Can you please provide details of your complete workflow?
Thank you for you comment.
My plan is described below:
Before running an RNA-seq, I don't have any data to estimate that.
Thank you in advance.
Do you need Step 4? I think that you should be doing:
Thank you very much for you kind advice.
After that, I obtained RNA-seq data and see if CPM varies or not.
As you mentioned above, I also confirmed that the CPM varies after ComBat-seq process.
I should read the original article carefully.
Thank you for your kind help.
Yes, it makes sense that the CPM values vary before and after ComBat-seq. ComBat-seq directly modifies the raw count values, meaning that any other calculation performed on these (including CPM (Counts per million)) will also be modified.