The genotype x time factorial experiment is a very common one, but I don't have any data of this type that I can make public. If anyone can provide a data example, or can suggest somewhere from where I can get a data example, then I'll put a detailed example in the the Limma User's Guide. Preferably one affy example and one two-color example. The probe IDs could be anonymized in some way but the data should relate to a real experiment. It seems that this would help a lot of people. Cheers Gordon At 05:59 AM 5/03/2004, Per Gregersen wrote: >I have a 2 x 3 factorial cDNA microarray experiment which I would like to >analyse in Limma. I need, however, some advise on the constuction of >design and contrast matrices - which is not straightforward to understand >for a non-statistician, as I am. > >The experiment comprise two wheat lines (A,B - transgenic and wild type) >with RNA samples harvested at 3 different time points (1,2,3 - >develomental stages). The hybridisation experiment has been conducted as a >circular loop: A1-->A2-->A3-->B3-->B2-->B1-->(and back to A1), and in >addition there is a dye swap between A2 and B2, to balance the dyes. In >total 8 arrays. > >I am primarily interested in the main effect of the transgene and any >interaction effects between line and time. Secondarily, the main effect of >time is also of interest, i.e. which genes go up or down between time1 and >time2, and between time2 and time3 for both lines. > >I hope, I can have some suggestions about the construction of design and >constrast matrices, in order to analyse these effects in the best way. > >Thanks. > >Per Gregersen >Department of Plant Biology >Danish Institute of Agricultural Sciences >DK-4200 Slagelse, Denmark