[BioC] Genotype x Time factorial experiments - a request for data

[Gordon Smyth]

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