[BioC] Obtain MAS5.0 Signal using affy

Isaac Neuhaus isaac.neuhaus@bms.com
Wed, 16 Oct 2002 09:27:09 -0400


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.



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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