[BioC] Affy: Present calls in an eset

Jenny Drnevich drnevich at uiuc.edu
Wed Oct 8 11:28:17 MEST 2003

> > 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"
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 :)


Jenny Drnevich, Ph.D.
Department of Animal Biology
515 Morrill Hall
505 S Goodwin Ave
Urbana, IL 61801

ph: 217-244-6826
fax: 217-244-4565
e-mail: drnevich at uiuc.edu

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