[BioC] dye effects stronger than dye-swaps?

[Jenny Drnevich]

Hi everyone,

I have an interesting phenomenon in some microarray data, and 
wondered if anyone else has seen anything like it. It's 2-color data, 
comparing mutant vs. wildtype, 2 replicates plus dye-swaps for a 
total of 4 arrays. The 'dye-swaps', instead of being negatively 
correlated in M-values are instead strongly positively correlated, 
even after within-array normalization. I triple checked to make sure 
I didn't have the phenotypic info wrong, but all of the arrays are 
positively correlated, which leads me to believe that dye-swapping 
wasn't actually done. If you analyze as if it were a dye-swap 
experiment, several thousands of genes still show a dye-effect, 
whereas only dozens of genes show a MUvWT effect.

My question: is it possible that any dye-effects could be so strong, 
even after within-array normalization, and treatment differences so 
small that the arrays could be dye-swaps but still show a positive 
correlation in M-values? Or is it more likely that dye-swapping 
wasn't actually done?  I've tried to look at other dye-swapped data, 
but everything I have has large treatment differences. The PI already 
has the manuscript written, and just came to me to 'confirm' their 
analysis, so I want to be pretty positive before I tell them their 
work may have been wasted (of course, they may still decide to ignore me...)

Thanks,
Jenny

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu