[BioC] cluster genes based on expression pattern

[Moshe Olshansky]

Hi Rabe,

You can check timecourse package (Bioconductor).
Sean's suggestion to filter genes is always a good idea.
My naive approach would be to define a sensible distance between two genes
and use this distance for clustering (one possibility is hclust).
To define a distance, suppose that you have two genes, A and B and n+1
time points: 0,1,...,n. Let Ai and Bi be expression levels of genes A and
B at time i (i=0,1,...,n). One possibility is just the Lp distance (for a
suitable p). Another possibility is to say that we do not care about the
absolute abundance but only about how it evolves in time and then we can
look at AAi = Ai/A1 and BBi = Bi/B1, i=1,2,...,n and take some Lp (or
other) distance between AA and BB.
These are just some suggestions. You may think of another reasonable
distance.

Best regards,
Moshe.

P.S. I would be interested to know what you have done and how well it
works (since we also sometimes come across such data but I never had time
to explore this).

> Hi all,
>
> I have a normalized microarray (Affy) gene expression data for different
> time points and i would like to cluster genes with similar expression
> pattern ,which package shall i use?
>
> Thanks in advance
> Best Regards,
> Rabe
>
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