[BioC] Affy: Present calls in an eset

[Rafael A. Irizarry]

fyi, 
we just put into the devel version of affy the method "mas5calls", that 
works on instance of AffyBatch and ProbeSet, that for AffyBatch returns an 
exprSet with  MAS 5.0 P,M,A calls in the exprs slot and the wilcoxon 
test pvalue in the se.exprs slot. According to our tests, The P,M,A calls 
reproduce affymetrix's almost perfectly. the p-values dont match up as well.

we would greatly appreciate feedback.

the engine function mas5.detection that works on nx2 matrices, was 
contributed by Ben Rubinstein

-r


On Wed, 8 Oct 2003, Rafael A. Irizarry wrote:

> 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
> > > 
> > > CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be
> > > confidential and privileged. If you received this message in error,
> > > please destroy it and notify the sender. Thank you.
> > >
> > 
> > _______________________________________________
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> > 
> 
> 

-- 
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| Rafael Irizarry			phone:	(410) 614-5157		|
| Assistant Professor			fax:	(410) 955-0958		|
| Department of Biostatistics		office: E3035			|
| Johns Hopkins University		email:	rafa at jhu.edu		|
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