[BioC] heatmap.2

[carol white]

How are they combined? So my formula was not correct? Any reference, documentation of the performed steps (general description and/or math description)?

Many thanks

--- 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
> >>
> >
> >
> >
> >
>