[BioC] Significant dye bias using limma

[Mark Pinese]

Hello all,

I have some questions regarding whether the significant dye bias I'm finding in
my analyses could be an artefact of my analysis method.

I've been using limma to analyse a simple design comparing treatment and control
cases using dye swaps.  As per suggestions in the recent limma Users' Guide,
I've added an intercept term to the design, and used it to find genes with
significant dye effects.  limma reports very many significantly dye-biased genes
(B-values as high as 12.7, 205 genes with B > 5), and very few significantly
differentially-expressed genes (highest B = 3.1).

I'm using three biological replicates, each hybridised to two dye-swapped arrays
as technical replicates, on Compugen human 19k cDNA slides.

Is such a strong result plausible, or due to me incorrectly analysing the data?
 If so, what major pitfalls could I have blundered into?  What sort of
diagnostics can I try to test how reliable the model results are?


Thanks for your time,

Mark Pinese