[BioC] limma Common Reference Analysis

[Khan, Sohail]

Hi, 
The following message was not posted properly.
I have analyzed a common reference with 4 groups experimental design by applying the same method described in the limma user's guide for common reference 2 groups. However, all of the reference samples were labeled with Cy5. Therefore I multiplied all of the resulted ratios with -1. Is this a valid approach? Thanks. 


Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076