CPM after ComBat-seq
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5 months ago
Gum ▴ 10

hi!

Are original CPMs modified after a batch correction with ComBat-seq?

(CPMs are re-calculated after the process)

Thank you

RNA-Seq • 312 views
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Please upvote and/or accept answers rather than adding titles like "closed" which have no meaning. Thank you.

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5 months ago

Most likely, yes. Can you please provide details of your complete workflow?

For example:

  1. normalisation of raw counts with EdgeR
  2. calculate CPM
  3. batch correction
  4. et cetera
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Thank you for you comment.

My plan is described below:

  1. RNAseq
  2. STAR mapping
  3. Htseq
  4. calculate CPM(= original CPM)
  5. ComBat-seq using raw count data
  6. calculate CPM

Before running an RNA-seq, I don't have any data to estimate that.

Thank you in advance.

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Do you need Step 4? I think that you should be doing:

  1. Run RNAseq experiment
  2. STAR mapping
  3. Htseq-count
  4. ComBat-seq using raw count data
  5. normalisation of batch-corrected raw counts
  6. calculate CPM
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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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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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