[BioC] question about output of edgeR

James W. MacDonald jmacdon at uw.edu
Wed Apr 9 20:46:48 CEST 2014

Hi Son,

The logCPM is just the overall log average over both groups. So you 
have the logFC, which tells you how different the two groups were, and 
the logCPM which tells you the average abundance, which is a way to 
assess the signal/noise ratio. In other words, the larger the logCPM, 
the more signal you have and consequently the less influence of noise.



On Wednesday, April 09, 2014 2:15:52 PM, Son Pham wrote:
> Dear edgeR community:
> In the output of edgeR for two groups testing:
> topTags(et, n=20), for example.
> We have:
> Gene ID    logFC     logCPM      pValue       FDR
> I wonder why we only have one column of logCPM, since this is a comparison,
> I think there should be two such columns, one for each sample?
> Probably that I misunderstood something here?
> Thanks,
> Son.
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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