[BioC] moderated t statistic in limma

[Jenny Drnevich]

Hi Pedro,

If you look at the code for 'ebayes', you'll see that the moderated t is 
calculated as:

out$t <- coefficients/stdev.unscaled/sqrt(out$s2.post)

However, when I check with the numbers you show, I don't get the same 
answer as your fit2$t[1] either, so I don't know what's going on with your 
data:

 > -0.0468 / 0.5774 / sqrt(0.5344)
[1] -0.1108756

Could a rounding issue make the resulting value that far off?

Best,
Jenny

At 06:32 AM 7/6/2006, Pedro López Romero wrote:


>Dear list
>
>I am trying to calculate the moderated t-statistic by hand for a given
>gene[i], and it is not equal to the moderated t value that eBayes ( )
>gives.-
>
>
>After fitting my model I can recover the following values for gene [1] :
>
> > fit$stdev.unscaled[1] # from lmFit (...,)
>[1] 0.5774
>
> > fit2$coeff[1] # from eBayes(...,)
>[1] -0.0468
>
> > fit2$s2.post[1]
>[1] 0.5344
>
> > fit2$t[1]
>[1] -0.1421
>
>
>and *manually* the moderated t-statistic is:
>
> > fit2$coeff[1]/(fit$stdev.unscaled[1]*fit2$s2.post[1])
>[1] -0.1517
>
>
>Did I do something wrong?
>
>Thanks a lot.-
>
>Pedro
>
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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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1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu