[BioC] Obtain MAS5.0 Signal using affy

Kenny Ye kye@ams.sunysb.edu
Wed, 16 Oct 2002 02:39:45 -0400 (EDT)

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 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