[BioC] clustering of microarray time-series data

Maciej Jończyk mjonczyk at biol.uw.edu.pl
Sat Oct 16 12:43:42 CEST 2010

>Message: 13
>Date: Fri, 15 Oct 2010 14:47:44 -0400
>From: avehna <avhena at gmail.com>
>To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>Subject: [BioC] clustering of microarray time-series data
><AANLkTim6Kiep+heAxQWj27CL9A-vsOQmpLAdL_a87==L at 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
>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
>across the time points to group the genes according to their expression
>My question is: what method should I use in order to do this? I have
>already the
>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

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

More information about the Bioconductor mailing list