Thank you Maciej. I will try it and let you know.

Avhena

2010/10/16 Maciej Jończyk <mjonczyk@biol.uw.edu.pl>

> >Message: 13
> >Date: Fri, 15 Oct 2010 14:47:44 -0400
> >From: avehna <avhena@gmail.com>
> >To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
> >Subject: [BioC] clustering of microarray time-series data
> >Message-ID:
> ><AANLkTim6Kiep+heAxQWj27CL9A-vsOQmpLAdL_a87==L@mail.gmail.com>
> >Content-Type: text/plain
> >
> >Dear All,
> >
> >I have a time series data from two different samples (treatment A and
> >treatment B) at 3 different time points (0 hr, 6 hr and 24 hr) , the
> control
> >is time = 0 hr. Both datasets have three replicates.
> >
> >I have already analyzed these data using limma, just to have an idea of
> >regulated genes at 6 hr and 24 hr, but now I would like to cluster the
> data
> >across the time points to group the genes according to their expression
> >profile.
> >
> >My question is: what method should I use in order to do this? I have
> checked
> >already the
> timecourse<
> http://www.bioconductor.org/packages/release/bioc/html/timecourse.html
> >package,
> >but I'm afraid it includes a different method for defining
> >differentially expressed genes (and I would like to be consistent with
> >limma's results). Any clue?
> >
>
> You can try analyse your data using MaSigPro package.
> It compares treatment profiles, draws plots of profiles and also
> clusters data.
>
> It don't give you contrasts between time points, but compare whole time
> profiles.
>
> Personally I don't use it for clustering, I tried pvclust R package but
> most probably I'll use JMP Genomics for this. Nevertheless I strongly
> recommend MaSigPro.
>
> >
> >
>
>
> Maciej Jończyk, MSc
> Department of Plant Molecular Ecophysiology
> Institute of Plant Experimental Biology
> Faculty of Biology, University of Warsaw
> 02-096 Warszawa, Miecznikowa 1
>
>
>
> ___________________________________
> NOCC, http://nocc.sourceforge.net
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>

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