[BioC] The reported bug in affy package persists

[Ben Bolstad]

This bug was addressed months ago. It certainly has been fixed in the
development versions. Try the development version. When I made my
comparison of MAS 5 values at

http://stat-www.berkeley.edu/~bolstad/MAS5diff/Mas5difference.html

I used the development version. Clearly the subtraction of the ideal
mismatch is occurring.

Ben


On Fri, 2003-04-18 at 13:35, Hongxian He wrote:
> Today I independently identified a bug in the pmcorrect.mas method from 
> "affy" package (v1.1.1), which has been posted on the mailing list before. 
> But I found that the bug is still in the lastest release of affy package, 
> and the results computed therefore disagree with MAS5. 
> 
> 
> pm.corrected <- apply(cbind(pps.pm, pps.im, delta), 1, max)
>   {
> 	...
> 	 pm.corrected <- apply(cbind(pps.pm, pps.im, delta), 1, max)
> 	...
>   }
> 
> Shouldn't the above line be 
> 
> 	pm.corrected <- apply(cbind(pps.pm - pps.im, delta), 1, max) 
> 
> according to the formula V_{i,j} = max(PM_{i,j} - IM_{i,j}, d) in 
> Affymetrix statistical algorithm document, where PV_{i,j}= log2(V_{i,j}), 
> PV_{i,j} is the probe value for probe pair j in probeset i?
> 
> Thanks,
> 
> Hongxian He
> Center of Bioinformatics
> University of Pennsylvania
> 
> 
> ==================================================================
> Quoted from the archive:
> 
> [BioC] the result of bioconductor not agree with MAS
> "Hüsing, Johannes" johannes.huesing at medizin.uni-essen.de
> Mon Mar 10 18:04:43 MET 2003
> 
> > -----Original Message-----
> > From: Ben Bolstad [mailto:bolstad at stat.berkeley.edu]
> > Sent: Thursday, March 06, 2003 5:48 PM
> > To: Lang Chen
> > Cc: 'bioconductor at stat.math.ethz.ch'
> > Subject: Re: [BioC] the result of bioconductor not agree with MAS
> > 
> > 
> > Hi Lang Chen (and to anyone else this is an issue for),
> > 
> > We have made our best attempts to duplicate the MAS 5.0 
> > algorithm using
> > available documentation. 
> 
> If I read the code in pmcorrect.mas() correctly (affy version 1.1), 
> the mismatch is not subtracted from the perfect match, so the line
> 
> pm.corrected <- apply(cbind(pps.pm, pps.im, delta), 1, max)
> 
> should IMHO rather read
> 
> pm.corrected <- apply(cbind(pps.pm-pps.mm, pps.im-pps.mm, delta), 1,
> max) ?
> 
> I might very well be missing something, so if somebody could give
> me a clue I'd be grateful.
> 
> Best regards
> 
> 
> Johannes
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>