[BioC] P calls

Rafael A. Irizarry ririzarr at jhsph.edu
Mon Mar 17 09:33:35 MET 2003

in my opinionm the main reason affy uses these is because MAS 5.0 has so
much noise at "the bottom". if they didnt, all their large fold changes
would be for genes with low expression. with RMA, what i use, you dont
have this problem so i dont see the need to throw away information. there
are other ways to get rid of the "noise" at the bottom: dChip (pm-only)
and vsn are two exaples.

There is no designated place to stick them into exprSet. you could create
another exprSet just for these or since MAS doesnt give SEs,
you could stick them in the se.exprs slot. a better (but you need to code
some) solution is to extend the exprSet class to a new class that includes
a slot for these calls.

On Mon, 17 Mar 2003, Stephen Henderson wrote:

> I'd like to use the Present (P) and Absent (A) calls for some rudimentary
> filtering of data prior to analysis. Is there an appropriate slot for
> inserting P and A calls within the exprSet object? 
> I'd like to garner opinions: Does anyone else use these , think them
> worthwhile, or perhaps use some other surrogate? 
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