[BioC] [limma] Design and contrast matrices question

Sean Davis sdavis2 at mail.nih.gov
Fri Nov 7 15:03:14 MET 2003

I am new to using limma.  I have a set of 2-channel experiments that I have
an interest in comparing. All are with respect to a common reference.  The
sets of samples that I have are:
Set 1 (10 slides) cell type 1
Set 2 (5 slides) cell type 2
Set 3 (2 slides) cell type 3
Set 4 (10 slides) mixture of cell type 3 (contamination, unavoidable) with
cell type 1 treated with x

I wish to form an appropriate design matrix and then find the contrasts
Cell type 1 and cell type 2
Cell type 1 and cell type 1 treated with x
Cell type 3 and (cell type 1 treated with x)

I am willing to assume that the amount of contamination is similar across
contaminated slides.

Thanks for any advice.

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