[BioC] diff (Beginner's question)

[peter robinson]

Dear all,

I have analyzed one data with (8 arrays of 4 wildtype and 4 ko) set basically 
according to the methods outlined in the End2Endlab vignette. The analysis 
includes a function:

scores <- esApply(eset,1,function(x) {
tmp <- t.test(x[index2],x[index1],var.equal=T)
c(mean(tmp$estimate),-diff(tmp$estimate),tmp$statistic,
tmp$p.value)
})


I would like to compare this with another dataset with one array each (pooled 
RNAs) wt vs ko (for a related gene being knocked out). 

I used the rma function to produce an eset of the second dataset, and then 
tried to use

e <- -diff(exprs(eset2))


in order to produce the average log ratio for the second dataset with the 
intention of adding it to "scores" as follows:

scores2 <- cbind(scores,e)

However, e is missing the first line as compared to the first dataset
dim(e)
12487  2
dim(scores)
12488   5
and in fact
100001_at  is missing from e.

I would greatly appreciate comments or suggestions!

Peter Robinson