[BioC] dye effects stronger than dye-swaps?

[Sean Davis]

On Monday 30 April 2007 14:36, Jenny Drnevich wrote:
> 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...)

Jenny,

Just a quick question--were the samples amplified?  

Sean