[BioC] Obtain MAS5.0 Signal using affy
Rafael A. Irizarry
rafa@jhu.edu
Wed, 16 Oct 2002 09:21:24 -0400 (EDT)
we have plans to do this but not to high in the to-do list.
obviously contributions are welcome.
rafael
On Wed, 16 Oct 2002, Kenny 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
>