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?

I will really appreciate any help from you.

Thank you!
Avhena

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