[BioC] analysis of timeseries with treatment effect

Carlos Calderon ccaldero at ira.cinvestav.mx
Wed Jul 5 03:42:27 CEST 2006

Bioconductor comunity:
I have been trying to find the best way to answer the classical questions for 
a timeseries with two treatment effect. Altough I have been reading I am not 
able to find an example about the best matrix design and contrasts in order to 
answer the above questions. 
If I use modelMatrix() using the targets frame I have got a matrix design that 
makes me able to identify genes with differential expression between 
treatments in a single time point. But about the second question, how the 
treatment changes across the timeseries? I'm not sure how to treat it. I guess 
that I need to analyze the interaction between time and treatment but my so 
poor experience using linear models and making contrasts limits my analysis, 
so I think I am not fully taking advantage of all the data.
The experiment is a two-color time series experiment, 4 time points, 2 
treatments, 16 arrays:

      II    II    II    II

2hybs per time point for direct comparisons (getting 8 slides) plus the other 
8 slides to make hybs across times, as indicated in the representation.
Thank you in advance.

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