[BioC] Subsetting Affybatch objects by gene lists.

[Horswell, Stuart]

Hi all,

	I'm trying to run an analysis on 24 Affymetrix HGu95v2 chips.

I've set up, via merge.AffyBatch, an affybatch object containing all 24 arrays.

A1 <- read.affybatch("A1.cel")
.
.
.
A24 <- read.affybatch("A24.cel")

A <- merge.AffyBatch(A1, A2)
A <- merge.AffyBatch(A, A3)
.
.
.
A<- merge.AffyBatch(A, A24)


 I then computed MAS5 type Present/Absent calls for each array using mas5calls.

A.calls <- mas5calls(A)
p.a.A <- exprs(A.calls)

 What I'd like to do now is remove all of those genes without a single present call across all 24 arrays before normalizing. 

I can use the p.a.A file to obtain a list of the gene names/affy id tags that I want to remove but I can't figure out how to delete the relavent probe pairs from my affybatch object. 

In fact that only things I've been able to find on the mailing list archive and/or vignettes are how to subset by array or how to remove chunks from the cdf environment - but this presents me with two problems, first I'm not sure I can get the pattern matching working well enough to identify which entry numbers in the cdf file correspond to the gene list I have, and secondly, people have already commented that this isn't neccessarily a sensible approach for proper analysis anyway. So I'm kind of stumped now!

Any help or advice would be most greatfully received,

     many thanks,

           Stu