[BioC] Affy: Present calls in an eset

[Jenny Drnevich]

> > Anyway, with MAS the calls are calculated anyway, can't they? So, I'd 
> be nice
> > (at least for "completness") to add a "mascall" method to the exprSet 
> objects
> > generated by affy. What do you think?
>
>It would be great.  As far as I know, the MAS calls are protected as a
>trade secret and non-disclosure agreements.  Maybe not, but I happen
>to know for sure that the rosetta resolver calls are! (or I'd have
>implemented them for amusement)

Actually, Affy is pretty open about their algorithms. See their 
"Statistical Algorithms Reference Guide"
http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf
However, their detection algorithm doesn't seem to tell you exactly how 
they calculate everything. Alternatively, we've been using a paired t-test 
on the raw PM and MM values in a chip (one-sided) and consider genes to be 
expressed/present where PM>MM. I haven't checked to see how our method 
compares to Affy's - maybe I will when I get some free time :)

Cheers,
Jenny







Jenny Drnevich, Ph.D.
Department of Animal Biology
515 Morrill Hall
505 S Goodwin Ave
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e-mail: drnevich at uiuc.edu