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 between: 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. Sean [[alternative HTML version deleted]]

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 >between: >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. Gordon >Sean