[BioC] How to decide which distance metric to use for micoarray data clustering?

Peng Yu pengyu.ut at gmail.com
Wed Oct 7 16:49:04 CEST 2009

Besides the distance metrics, there are other things that may also be
important. For example, multiple probesets map to a same gene. I can
do clustering on probeset values or on averaged probeset values of
genes. What factors should I consider when I make this kind of

bioDist says something about two popular metrics, but the description
is distilled. I am wondering whether there are some more detailed
comparisons between metrics.

On Wed, Oct 7, 2009 at 12:35 AM, Tim Triche <tim.triche at gmail.com> wrote:
> look at the bioDist package for some suggestions.
> the metric to use depends on your task.
> On Tue, Oct 6, 2009 at 8:52 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> Hi,
>> I am looking for the most appropriate distance metrics for the
>> clustering of a set of microarray data. And I read Chapter 12 of
>> Bioinformatics and Computational Biology Solutions Using R and
>> Bioconductor, But I'm still not clear what the general guide line is
>> to choose an appropriate distance metrics out of many ones list in
>> that chapter. Could somebody let me know how to choose an appropriate
>> distance metrics?
>> Regards,
>> Peng
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> --
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> models.
> --George Box

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