[BioC] [limma] Design and contrast matrices question

Gordon Smyth smyth at wehi.edu.au
Sat Nov 8 00:13:23 MET 2003

At 01:03 AM 8/11/2003, Sean Davis wrote:
>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.

Please read Limma User's Guide Section 7.3.



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