[BioC] p-value difference between R-affy and MAS5

[t-kawai at hhc.eisai.co.jp]

Hi,

mas5calls function is very usefull for getting p-values and P/M/A calls.

I have been wondering about the discrepancy between p-value of R-affy and
that of original MAS5.  Today I found the reason.

R-affy performs Wilcoxon test on (PM-MM) vs tau (default 0.015), on the
other hand, MAS5 performs Wilcoxon test on (PM-MM)/(PM+MM) vs tau value.
In my case, for example, p-values of AB000115_at were 0.018281 and
0.046482, respectively, and Detection Calls resulted in "P" and "M".

Is this bug, or not?




_______________________________________

Takatoshi Kawai, Ph.D.

Senior Sientist, Bioinformatics
Laboratoy of Seeds Finding Technology
Eisai Co., Ltd.
5-1-3 Tokodai, Tsukuba-shi,
Ibaraki 300-2635, Japan

TEL: +81-29-847-7192
FAX: +81-29-847-7614
e-mail: t-kawai at hhc.eisai.co.jp