[BioC] Limma without eBayes correction

Jenny Drnevich drnevich at illinois.edu
Fri Jan 30 16:18:15 CET 2009

Hi Daniel,

I have had to do this occasionally. See section 10.2, Fitted Model 
Objects. It shows how to get the ordinary t-stats from the fit object 
after calling just lmFit().  This is how ebayes calculates the 
p-values, so just substitute in the ordinary t-values and fit$df.residual:

out$p.value <- 2 * pt(-abs(out$t), df = df.total)


At 09:02 AM 1/30/2009, Daniel Brewer wrote:
>I normally use the eBayes correction and I am very happy about it, but I
>am trying to check some analysis performed by someone else and they used
>straight linear models with no correction.  I am no its not recommended,
>but its the situation I have to deal with.
>How do I use limma without eBayes?  I read somewhere that it is in the
>Limma's user guide but I can't for the life of me find it.
>Daniel Brewer, Ph.D.
>Institute of Cancer Research
>Molecular Carcinogenesis
>Email: daniel.brewer at icr.ac.uk
>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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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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