[BioC] Normalization of single color Agilent Arrays

[Lana Schaffer]

Hi,
I have some Agilent RNA data for which there are
only 2 conditions and single color and each condition
is applied to separate chips.  Without scaling I got
a 10,000 of differentially expressed genes with less
than 8% FDR.  After scaling the number of differential
genes decreased to ~6,000 with less than 16% FDR.  The
chips obviously need to be scaled.  Does anyone have any 
recommendations for normalization?

Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer at scripps.edu