[BioC] Obtain MAS5.0 Signal using affy

[Kenny Ye]

Ben and Julien, thanks for pointing me to this document. glad that they
removed it from ``confidential''.

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

On 16 Oct 2002, Ben Bolstad wrote:

> 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
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 
>