# [BioC] Obtain MAS5.0 Signal using affy

**Isaac Neuhaus
**
isaac.neuhaus@bms.com

*Wed, 16 Oct 2002 09:27:09 -0400*

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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