[BioC] Affy: Present calls in an eset

[Arne.Muller at aventis.com]

That's great news, Rafael! Thanks!

The absent/present calls are already included in the TXT files from the Affy
software (based on MAS). I was wondering if it's possible to getse files into
the Bioconductor affy package. This's be some kind of high level analysis,
since the "summary" per gene (the intensity) is already calculated by the
Affymetrix software based on PM/MM.

As understand the Bioconductor affy package, the normalisation is done one
the probeset level (for each of the 40 oligos per gene), rather than the
gene's intensity (affy normalisation is done *before* the probesets are
summarised into genes). This is somehow different of what we (and others) do
- although I guess it's a good idea to perform normalisation at the "lowest"
end, ie he probesets. Is it possible to apply the "normalize.methods" to
background + pm corrected and summarised genes; i.e.

1. read probe level data
2. background corredtion
3. probe specific bg correction (e.g. substracting MM)
4. Summarizing the probe set values into one expression value
5. normalize summarized expression values

	kind regards,

	Arne

> -----Original Message-----
> From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu]
> Sent: 08 October 2003 16:54
> To: Muller, Arne PH/FR
> Cc: rossini at u.washington.edu; bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] Affy: Present calls in an eset
> 
> 
> we will *try* to have mascall fro the next release.
> 
> On Wed, 8 Oct 2003 Arne.Muller at aventis.com wrote:
> 
> > Hi,
> > 
> > I get your point with interpreting absent/present calls. 
> Technically it's a
> > nice feature, becasue one can just discard the majority of 
> the genes on the
> > chip for further analysis. In fact I think absent/present 
> calls make sense in
> > terms of biology, since just a fraction of the genes are 
> realy expressed at a
> > time. How to express this numerially is a different story 
> (and I guess a
> > difficult one).
> > 
> > Anyway, with MAS the calls are calculated anyway, can't 
> they? So, I'd be nice
> > (at least for "completness") to add a "mascall" method to 
> the exprSet objects
> > generated by affy. What do you think?
> > 
> > By the way, if you ignore the call, do you set an arbitrary 
> intensity cutoff
> > later in your analysis, or do just reley on the statistics 
> (anova  p-value or
> > whatever)?
> > 
> > 	regards,
> > 
> > 	Arne
> > 
> > 
> > > -----Original Message-----
> > > From: A.J. Rossini [mailto:rossini at blindglobe.net]
> > > Sent: 08 October 2003 15:33
> > > To: Muller, Arne PH/FR
> > > Cc: bioconductor at stat.math.ethz.ch
> > > Subject: Re: [BioC] Affy: Present calls in an eset
> > > 
> > > 
> > > <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
> > > UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail 
> is unreliable
> > > FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email
> > > 
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