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Old 01-28-2013, 05:40 PM   #1
danielfortin86
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Default EdgeR cpm values after batch effects

Is there a way to obtain the CPM values from EdgeR after batch correction? The "cpm" function only returns values after library size normalization. When I look at the result of glmFit there are "abundance" "fitted.values" and "counts". The description in the documentation (?glmFit) is not entirely clear to me. Are the "fitted.values" cpm values after batch correction or should I be doing something else?

Thanks!
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Old 02-01-2013, 03:22 PM   #2
Gordon Smyth
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The answer is probably yes, but this is quite a technical question that can probably only be answered by the package authors, so it would best be sent to the main edgeR help list. See "how to get help" in the edgeR User's Guide.
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Old 08-25-2013, 09:58 AM   #3
gfmgfm
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Default CPM after batch effect correction in edgeR

Hello,

I wonder if you figured out how to print CPM after batch effect correction. I am trying to do exactly the same.

Many thanks.
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Old 08-25-2013, 08:58 PM   #4
Gordon Smyth
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You could try:

library(edgeR)
logCPM <- cpm(y, log=TRUE, prior.count=3)
logCPM <- removeBatchEffect(y, batch=batch)

Otherwise, follow the advice given in my earlier post.
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Old 08-25-2013, 09:12 PM   #5
gfmgfm
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Thank you. This is very helpful!
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