CPM after ComBat-seq
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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
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Kevin Blighe
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
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Kevin Blighe
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.
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