[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


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