[BioC] Finding and controlling for dye bias in Limma
Sean Davis
sdavis2 at mail.nih.gov
Thu Sep 9 12:35:24 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? 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
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