[BioC] Obtain MAS5.0 Signal using affy

[Ben Bolstad]

You can find a full description of MAS5.0 (or at least the most complete
I have seen) at 

http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

Ben


> Kenny:
> 
> A full description of the algorithm has been released by  Affymetrix. I have
> a perl version of MAS 5.0 and I will make it available as soon as Affymetrix
> agrees to it.
> 
> Regards,
> 
> Isaac
> 
> Ye wrote:
> 
> > has anyone wrote a function for the MAS5.0 signal measure in affy? I am
> > processing DAT files of some customized chips, and couldn't find the CIF
> > file that MAS requires. As the CDF file is available, I am able to process
> > DAT files and obtain CEL files using dChip, then import everything to
> > affy. Interesting how dChip does it without the CIF file but MAS insists
> > on it.
> >
> > I looked at Hubbell's powerpoint file on Terry's website, but the
> > equations given there are quite confusing. It shouldn't be difficult to
> > write the function as long as the formulae are set straight. following is
> > my best guess
> >
> > Signal = Average of Tukey_Biweight(log(PM-CT))
> >
> > if MM < PM, CT=MM
> > if MM > PM, CT=PM/exp(proportion)
> >
> > proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs
> > on the chip or just the set?). proportion is set to be 0 if the
> > average is negative.
> >
> > However, one still need to decide the support of the Tukey_Biweight
> > function. Maybe that doesn't matter much. Or simply take the
> > median. I don't understand why affymetrix doesn't want to disclose
> > their algorithm completely.
> >
> > Thanks in advance for your suggestions.
> >
> > Kenny
> >
> > Kenny Ye
> > Assistant Professor
> > Department of Applied Math and Statistics
> > SUNY at  Stony Brook
> > Stony Brook, New York 11794-3600
> > Phone (631)632-9344
> > Fax   (631)632-8490
> >
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> > Bioconductor@stat.math.ethz.ch
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> 
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