[BioC] Differential expression in time series

[James W. MacDonald]

Hi Peter,

Peter Robinson wrote:
> Hi,
> 
> I was wondering if anyone could give me pointers for the following
> situation. Given a time course data series with 3-4 repeats for
> individual time points, what is the best way of determining a list of
> differentially expressed genes for each time point (possibly compared
> to the zero time point)? I can think of several ways of going about
> this, but I have not been able to find very much in the literature I
> have consulted (perhaps I am looking in the wrong place).

Have you looked at the limma user's guide? There is at least one example 
of a time course analysis there. You might also use the BioC taskViews 
pages. For instance, there is one for TimeCourse experiments here:

http://www.bioconductor.org/packages/2.0/TimeCourse.html

Best,

Jim


> 
> Thanks in advance, Peter
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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