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_whitepa per.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 > > >