Question: CPM after ComBat-seq
0
gravatar for Gum
10 weeks ago by
Gum10
Gum10 wrote:

hi!

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

(CPMs are re-calculated after the process)

Thank you

rna-seq • 211 views
ADD COMMENTlink modified 9 weeks ago by ATpoint46k • written 10 weeks ago by Gum10

Please upvote and/or accept answers rather than adding titles like "closed" which have no meaning. Thank you.

ADD REPLYlink written 9 weeks ago by ATpoint46k
3
gravatar for Kevin Blighe
10 weeks ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k wrote:

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
ADD COMMENTlink written 10 weeks ago by Kevin Blighe71k

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.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Gum10
2

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
ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Kevin Blighe71k

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.

ADD REPLYlink written 9 weeks ago by Gum10
1

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.

ADD REPLYlink written 9 weeks ago by Kevin Blighe71k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1359 users visited in the last hour
_