[BioC] Affy: Present calls in an eset

[A.J. Rossini]

<Arne.Muller at aventis.com> writes:

> Hello,
>
> I'm quite new to Bioconductor/affy, and I was wondering if there's a simple
> way to include the absent/present call for a gene in the outputfile generated
> with write.exprs(eset, file='boo') in theaffy package.
>
> the eset was generated with
>
> eset <- expresso(cel, bgcorrect.method = 'rma', normalize.method =   
>              'qspline', pmcorrect.method = 'pmonly', 
>              summary.method='liwong')
>
> For further analyses I'd like to exclude genes that are absent in all chips.

That's tough.  It isn't clear what a sensible definition of absent
is.  Or present.  

Do you mean "expressed" ?  "Differentially expressed" ?  "sort of
differentially expressed but not too weakly expressed?".  For any of
these, you'll need a precise definition (there isn't any in
Bioconductor), and you can compute your own.

(I know that MAS will make these calls; I'm only familiar with Rosetta
Resolver's variant, and they don't really make sense to me -- to be
precise, I know numerically how they are derived, but fail to why they
realistically connect biologically or technologically without a great
deal of assumptions and a wild imagination).

best,
-tony

-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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