[BioC] heatmap.2

[Sean Davis]

On Wed, Apr 28, 2010 at 4:01 PM, carol white <wht_crl at yahoo.com> wrote:
> How are they combined? So my formula was not correct? Any reference, documentation of the performed steps (general description and/or math description)?

The columns are ordered according to a dendrogram produced for the
samples; the rows are ordered according to a dendrogram produced for
the genes.  There is no "combination" that occurs.  One of the first
papers describing heatmaps applied in a microarray context is here:

http://www.ncbi.nlm.nih.gov/pubmed/9843981

Hope that helps.

Sean

> --- On Wed, 4/28/10, Sean Davis <seandavi at gmail.com> wrote:
>
>> From: Sean Davis <seandavi at gmail.com>
>> Subject: Re: [BioC] heatmap.2
>> To: "carol white" <wht_crl at yahoo.com>
>> Cc: bioconductor at stat.math.ethz.ch
>> Date: Wednesday, April 28, 2010, 12:56 PM
>> On Wed, Apr 28, 2010 at 3:52 PM,
>> carol white <wht_crl at yahoo.com>
>> wrote:
>> > Thanks Sean for your reply.
>> >
>> > Actually the question was not on the distance measure.
>> What I wanted to know how the clustering is performed on two
>> dimensions. Is the dissimilary function (whatever it is,
>> euclidean, pearson correlation, etc) is performed on all
>> variables and then, on the observations or any other way?
>> >
>> > Is it more clear?
>>
>> Sorry I misunderstood.  The clustering is done
>> independently in each
>> dimension.  The plot is where the two dimensions are
>> combined.
>>
>> Sean
>>
>>
>> > --- On Wed, 4/28/10, Sean Davis <seandavi at gmail.com>
>> wrote:
>> >
>> >> From: Sean Davis <seandavi at gmail.com>
>> >> Subject: Re: [BioC] heatmap.2
>> >> To: "carol white" <wht_crl at yahoo.com>
>> >> Cc: bioconductor at stat.math.ethz.ch
>> >> Date: Wednesday, April 28, 2010, 3:55 AM
>> >> On Wed, Apr 28, 2010 at 4:36 AM,
>> >> carol white <wht_crl at yahoo.com>
>> >> wrote:
>> >> > Hi,
>> >> > Does heatmap.2 function combine all variables
>> into a
>> >> single overall measure of dissimilarity between
>> two
>> >> observations as explained in The elements of
>> statistical
>> >> learning, Hastie et al, 2001, pp457? Does this
>> function
>> >> calculate the dissimilarity between observations
>> and
>> >> variables as follows?
>> >> >
>> >> >         N   N    p
>> >> > 1/(N^2) sum sum   sum d(xij,xi'j)
>> >> >        i=1 i'=1  j=1
>> >> >
>> >> > where N is the number of observations, p the
>> number of
>> >> variables, xi and xi' are two different
>> observations, and d
>> >> is the dissimilarity between two variables,
>> respectively.
>> >> >
>> >> > Any relevant information is welcome.
>> >>
>> >> Hi, Carol.
>> >>
>> >> The first place to stop when asking these types
>> of
>> >> questions is the
>> >> help system.  help(heatmap.2) shows that the
>> default
>> >> distance function
>> >> used is "dist".  Checking help(dist) reveals
>> that
>> >> there are many
>> >> options for distance measurement, but the default
>> is
>> >> "euclidean".
>> >> There are a number of examples and even a couple
>> of
>> >> references.
>> >>
>> >> Hope that helps.
>> >>
>> >> Sean
>> >>
>> >
>> >
>> >
>> >
>>
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