[BioC] analysis of timeseries with treatment effect
ccaldero at ira.cinvestav.mx
Wed Jul 5 03:42:27 CEST 2006
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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