[BioC] Limma - avereps - problems with NA

[Gildas Le Corguillé]

Hi,


I have a question about the function avereps in the limma package.
When I compare the relative outputs of this function in limma.2.18.2 and 
in the last version limma.3.6.6, I find different results.

If we take for example a gene with two probes :
  - probe1$M = 2
  - probe2$M = NA

The results will be :
  - for limma.2.18.2 : 2
  - for limma.3.6.6 : 1

The codes are :
  - for limma.2.18.2 :
             for (i in 1:length(u)) y[i,] <- 
colMeans(x[ID==u[i],,drop=FALSE],na.rm=TRUE)
  - for limma.3.6.6 :
             rowsum(x,ID,reorder=FALSE,na.rm=TRUE)/as.vector(table(ID))

So :
  - for limma.2.18.2 :
	colMeans(as.matrix(c(2,NA)),na.rm=TRUE)
             [1] 2
   - for limma.3.6.6 : (2 + 0) / 2 = 1
	rowsum(as.matrix(c(2,NA)),c(1,1),na.rm=TRUE)/as.vector(table(c(1,1)))
               [,1]
             1    1

For me, NA don't mean 0, so do you agree with me ?

Cheers

Gildas