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? 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? Thanks, Sean

> 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