[BioC] moderated t statistic in limma
Pedro López Romero
plopez at cnic.es
Thu Jul 6 13:32:12 CEST 2006
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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