[BioC] analysis of timeseries with treatment effect

Gordon Smyth smyth at wehi.EDU.AU
Thu Jul 6 12:39:00 CEST 2006

Dear Carlos,

There is a section in the limma User's Guide called "Time Course 
Experiments". Although the example given there is for Affymetrix 
arrays, have you tried adapting it to your situation?

Best wishes

>Date: Wed, 5 Jul 2006 01:42:27 +0000 (UTC)
>From: Carlos Calderon <ccaldero at ira.cinvestav.mx>
>Subject: [BioC] analysis of timeseries with treatment effect
>To: bioconductor at stat.math.ethz.ch
>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:
>       t1--->t2--->t3--->t4--->t1
>       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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