[BioC] Limma: eBayes makes p-values larger

James W. MacDonald jmacdon at med.umich.edu
Tue Oct 30 17:12:44 CET 2007

Daniel Brewer wrote:
> 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.

Some of the p-values or _all_ of the p-values? I would be surprised if 
all the p-values are larger - some should get smaller as well.

> Arising from this I have a few questions:
> 1) When should use the eBayes estimate and when should you not?

If you are using limma, IMO you should always use eBayes(). If you have 
very few samples, this will help. If you have many samples it won't 
hurt, and it is fast enough that the cost of doing so is minimal.

> 2) Is there anything wrong with using the results from using t.test and
> multtest?

Depends on how many samples you have. If you have enough samples that 
you can get a reasonable number of combinations, then the empirical null 
distribution from multtest should give good results, and you can argue 
that the empirical null is better than assuming normality of your data 
and using the t-distribution as the null. However, at some point the 
central limit theorem will kick in and you don't have to assume anything 
anyway ;-D.

So if you have lots of replication either e.g., rowttests() in Biobase 
or the multtest functions are great. However, if you don't have many 
replicates I think you can argue that limma is better.

> 3) Is there a way to use limma without using the eBayes correction?

Yes. IIRC, Gordon even mentions how to do it in the limma User's Guide, 
along with the advice that you shouldn't do it.



> Many thanks
> Dan

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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