[BioC] Limma 2.9.10: "Amean" missing

[Julien Gagneur]

Hi,

I miss the Amean field in the output of eBayes() in limma 2.9.10 .

It is there in limma 2.8.1

sample code:

#  Simulate gene expression data,
#  6 microarrays and 100 genes with one gene differentially expressed
set.seed(2004); invisible(runif(100))
M <- matrix(rnorm(100*6,sd=0.3),100,6)
M[1,] <- M[1,] + 1
fit <- lmFit(M)

#  Ordinary t-statistic
par(mfrow=c(1,2))
ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma
qqt(ordinary.t,df=fit$df.residual,main="Ordinary t")
abline(0,1)

#  Moderated t-statistic
eb <- eBayes(fit)


# this returns FALSE with limma 2.9.10, TRUE with limma 2.8.1
"Amean" %in% names(eb)



I run R 2.4.1. Do you experience the same?

Thanks,
Julien.

-- 
Julien Gagneur
EMBL/HTFG Center
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