[BioC] Subsetting Affybatch objects by gene list.

[Matthew Hannah]

Stu,

I'm abit confused as to why you want to go to so much trouble to subset your data.
RMA or any of the expresso functions can be called on the entire affybatch and then 
written to file. I don't see how this would be any different to the MAS5 analysis
you presumably want consistency with as MAS5 scales/normalises on a whole chip basis
anyway.

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.

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