[BioC] combining GSA and lmFit

Dick Beyer dbeyer at u.washington.edu
Mon Apr 27 05:43:28 CEST 2009

Hi All,

I have extended the GSA code (http://www-stat.stanford.edu/~tibs/GSA/) to include lmFit() from the limma package so as to have linear model capabilities with GSA.  Basically, I'm using the modified t-statistic values from lmFit just like the SAM-like t-statistic values are used in the GSA code.

I was wondering if anyone had any thoughts on whether this was, in principle, an OK thing to be doing.  I am worrying about whether there is an underlying issue I'm not aware of in using the moderated t-statistic values from limma as opposed to the SAM t-statistic values that uses the s0 term in the denominator.

My tests on some microarray data I have shows that in a qqplot of t-statistic values from the two methods, they are in pretty close agreement except for large values of the t-values.

If anyone knows of reasons not to be doing this or could point me to places with possible explanations, I'd be very grateful.


Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099

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