[BioC] Affy: Present calls in an eset

[paul.boutros at utoronto.ca]

I actually asked about this a while back:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-August/002081.html

The algorithms aren't too hard to code, although I haven't found the time to 
try it yet.

Overall, I don't think the calls are particularly valuable: as Tony says, if 
you read the algorithm you start to wonder at how arbitrary it all is.  On the 
other hand, I agree that it would be nice to be replicate this part of MAS5 
with Affy.

Paul


-----Original Message----- 
Date: Wed, 8 Oct 2003 15:47:42 +0200 
From: <arne.Muller at aventis.com> 
Subject: RE: [BioC] Affy: Present calls in an eset 
To: <rossini at u.washington.edu> 
Cc: bioconductor at stat.math.ethz.ch 
Message-ID: 
        
<C80ECAFA2ACC1B45BE45D133ED660ADE410B0E at crbsmxsusr04.pharma.aventis.com> 
         
Content-Type: text/plain;        charset="iso-8859-1" 

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 
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