3
Kevin Blighe ♦ 71k wrote:
Most likely, yes. Can you please provide details of your complete workflow?
For example:
- normalisation of raw counts with EdgeR
- calculate CPM
- batch correction
- et cetera
Thank you for you comment.
My plan is described below:
- RNAseq
- STAR mapping
- Htseq
- calculate CPM(= original CPM)
- ComBat-seq using raw count data
- calculate CPM
Before running an RNA-seq, I don't have any data to estimate that.
Thank you in advance.
2
Do you need Step 4? I think that you should be doing:
- Run RNAseq experiment
- STAR mapping
- Htseq-count
- ComBat-seq using raw count data
- normalisation of batch-corrected raw counts
- calculate CPM
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.
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