[BioC] limma and ebayes : error message : differences in versions?

[Sue Jones]

I have used limma to calculate differential gene expression (see code at 
end of message). I am currently using R 2.7, Biobase 2.0.1 and Limma 
2.14.6 and get the error message

Warning message:
Zero sample variances detected, have been offset

after uisng eBayes.

I know a previous message to this list explains this and says it 
can be ignored.

However, I conducted the same analysis using older versions of R, Limma 
and Biobase and did not see this message and got a much larger list of 
differentially expressed genes. Using the current versions of limma and 
biobase I see this message and my list of differentially expressed genes
is smaller - can this be correct?

Thanks for anyones help.


Code
------------------------------------------------------
> files <- c("W05h_1.CEL", "W0h_1.CEL", "W2h_1.CEL",
+ "W2h_2.CEL", "W4h_1.CEL",  "GW_025.CEL", "GW_1.CEL", 
"GW_3.CEL","E2h_1.CEL",  "E2h_2.CEL",
+ "E2h_3.CEL", "E2h_4.CEL")
> Data <- ReadAffy(filenames = files)
> Data_gcrma <- gcrma(Data)
> design<- cbind(WAT=c(1,1,1,1,1,1,1,1,0,0,0,0), ETH=c(0,0,0,0,0,0,0,0,1,1,1,1))
> fit <- lmFit(Data_gcrma,design)
> cont.matrix <- makeContrasts(WATvsETH=ETH-WAT, levels=design)
> fit2<- contrasts.fit(fit,cont.matrix)
> fit3 <- eBayes(fit2)
Warning message:
Zero sample variances detected, have been offset


Sue Jones
University of Sussex