EdgeR cpm values after batch effects

danielfortin86 · 01-28-2013, 05:40 PM

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!

Gordon Smyth · 02-01-2013, 03:22 PM

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.

gfmgfm · 08-25-2013, 09:58 AM

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.

Gordon Smyth · 08-25-2013, 08:58 PM

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.

gfmgfm · 08-25-2013, 09:12 PM

Thank you. This is very helpful!

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01-28-2013, 05:40 PM	#1
danielfortin86 Junior Member Location: California Join Date: Aug 2008 Posts: 5	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!

08-25-2013, 09:58 AM	#3
gfmgfm Member Location: il Join Date: Jun 2010 Posts: 64	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.

02-01-2013, 03:22 PM	#2
Gordon Smyth Member Location: Melbourne, Australia Join Date: Apr 2011 Posts: 91	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.

08-25-2013, 08:58 PM	#4
Gordon Smyth Member Location: Melbourne, Australia Join Date: Apr 2011 Posts: 91	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.

08-25-2013, 09:12 PM	#5
gfmgfm Member Location: il Join Date: Jun 2010 Posts: 64	Thank you. This is very helpful!