[BioC] Subsetting Affybatch objects by gene list.

[Rafael A. Irizarry]

> If you import into excel and then paste in the corresponding P/A calls from the MAS5
> software and a quick use of the IF and sort functions in excel perform your filtering.
> (especially as BioC P/A could be (very?) slightly different to MAS5). If you want to 
> use BioC/R for more analysis you could save the result to a txt file and then just read 
> it back into R.

or better yet use the save and load commands. faster and less typing. for
example
x <- ReadAffy()
save(x,file="x.rda",compress=TRUE)
rm(x)
load("x.rda")

##now x is back

> 
> A better thing to look into may be whether you really want to filter based on the P/A 
> calls as with RMA you might find that including A genes only has a very small effect on
> your final list of genes (if based on fold change). And thats before considering if
> the P/A call is useful due to the 1/3 of MM>PM.
> 
> Cheers,
> Matt
> 
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