[BioC] Limma without eBayes correction

[Holger Schwender]

Or alternatively use the standard R-functions lm or lm.fit for performing a linear regression in R. (x is the design matrix and y is the transpose of the matrix containing the signals.)

Holger


-------- Original-Nachricht --------
> Datum: Fri, 30 Jan 2009 09:18:15 -0600
> Von: Jenny Drnevich <drnevich at illinois.edu>
> An: Daniel Brewer <daniel.brewer at icr.ac.uk>, Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
> Betreff: Re: [BioC] Limma without eBayes correction

> 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)
> 
> Cheers,
> Jenny
> 
> At 09:02 AM 1/30/2009, Daniel Brewer wrote:
> >Hi,
> >
> >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.
> >
> >Thanks
> >
> >Dan
> >
> >--
> >**************************************************************
> >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 
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> >
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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
> 
> 330 ERML
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> 
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