[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.
Best,
Jim
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.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099
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