[BioC] Limma: eBayes makes p-values larger

[Daniel Brewer]

If I remember rightly, eBayes is used to estimate the variance of
expression for individual genes based on the expression profile of all
the genes as a whole.  I have a situation where I perform limma with
eBayes and have repeated it using t.test and the multtest library (so
without variance estimation) and have found that the p.values from limma
are larger than those found using the traditional approach.

Arising from this I have a few questions:
1) When should use the eBayes estimate and when should you not?
2) Is there anything wrong with using the results from using t.test and
multtest?
3) Is there a way to use limma without using the eBayes correction?

Many thanks

Dan


-- 
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Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk
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The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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