[BioC] moderated t statistic in limma
drnevich at uiuc.edu
Thu Jul 6 18:26:29 CEST 2006
If you look at the code for 'ebayes', you'll see that the moderated t is
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$t either, so I don't know what's going on with your
> -0.0468 / 0.5774 / sqrt(0.5344)
Could a rounding issue make the resulting value that far off?
At 06:32 AM 7/6/2006, Pedro López Romero wrote:
>I am trying to calculate the moderated t-statistic by hand for a given
>gene[i], and it is not equal to the moderated t value that eBayes ( )
>After fitting my model I can recover the following values for gene  :
> > fit$stdev.unscaled # from lmFit (...,)
> > fit2$coeff # from eBayes(...,)
> > fit2$s2.post
> > fit2$t
>and *manually* the moderated t-statistic is:
> > fit2$coeff/(fit$stdev.unscaled*fit2$s2.post)
>Did I do something wrong?
>Thanks a lot.-
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>Bioconductor at stat.math.ethz.ch
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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
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at uiuc.edu
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