[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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