[BioC] Two populations on microarray

[Ben Tupper]

Hello,

By virtue of experiment design we have two populations to analyze on each of a suite of Genepix microarrays.  You can see an example in an MA plot here (generated using the excellent limma package) :

	http://dl.dropbox.com/u/8433654/BE%20T46h%20slide%2052.png

We have been following the steps in the limma user guide, and Ben Bolstad's helpful notes http://tinyurl.com/7346mh9  All of the examples we see appear to have just one population to contend with, which gives us an inkling that we are being naive about our analysis.  We suspect that we'll have to separate the two populations before normalization and analysis.  Are there any guides available for managing two populations like this?

Thanks!
Ben


Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine   04575-0475 
http://www.bigelow.org