[BioC] Limma and time-course data

[Ana Conesa]

Dear Michael,

You might want to have a look at the package maSigPro for the analysis of 
microarry time-course data. The method evaluates differences in gene 
expression along time and between experimetal conditions without focussing 
on specific time points, but analyzing gene expression trends.

Ana


On Tue, 28 Feb 2006 12:30:47 -0000, michael watson \(IAH-C\) wrote
> Hi
> 
> Googling the list shows this up to be a rather hot topic, but I just
> wanted to ask a few more questions.
> 
> Firstly, it seems the plan for tackling time course data within 
> limma is to treat each time-point/treatment combination as a 
> coefficient to be estimated.  Thus, to ask "which genes are changing 
> over time", one must fit contrasts that compare every single time 
> point to every other time point, pairwise, and look for any gene 
> that is significant in one or more of those comparisons.  Is that correct?
> 
> I am also a tad confused by the documentation, which states (on page
> 47):
> 
> "> cont.wt <- makeContrasts(
> + "wt.6hr-wt.0hr",
> + "wt.24hr-wt.6hr",
> + levels=design)
> > fit2 <- contrasts.fit(fit, cont.wt)
> > fit2 <- eBayes(fit2)
> 
> Any two contrasts between the three times would give the same result.
> The same gene list
> would be obtained had "wt.24hr-wt.0hr" been used in place of
> "wt.24hr-wt.6hr" for example."
> 
> I'm confused why "wt.24hr-wt.0hr" and "wt.24hr-wt.6hr" would give the
> same gene list.  The first looks for differences in wt between time
> points 0 and 24, and the second looks for differences between time
> points 6 and 24.
> 
> I guess, to me, this all seems a bit verbose and difficult, particularly
> for large time-course experiments where many biologists want to 
> subset their data to those genes that change over time and thus want 
> to ask the question "does time have an effect on the expression of 
> my gene?" and are not particularly bothered, at this stage, which 
> particular time points those genes differ at.
> 
> Thanks in advance
> 
> Mick
> 
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