[BioC] Finding and controlling for dye bias in Limma
Gordon K Smyth
smyth at wehi.EDU.AU
Thu Sep 9 14:01:22 CEST 2004
> We have several samples hybed on two-color arrays (treated versus
> untreated). Half are in dye-swap. Can we use Limma to estimate the
> effect of dye-bias?
Yes
> A design matrix might look something like:
>
> Array Treatment Dye-bias
> 1 1 0
> 2 1 0
> 3 1 0
> 4 1 0
> 5 -1 1
> 6 -1 1
> 7 -1 1
> 8 -1 1
>
> The second coefficient would be significant for "dye-biased genes"
> while the first would be treatment effect while controlling for dye
> bias? Do I understand correctly?
No, the Dye-bias column should be all 1's.
Gordon
> Thanks,
> Sean
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