[BioC] Affy: Present calls in an eset

[Rafael A. Irizarry]

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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> 
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