[BioC] heatmap.2

[Sean Davis]

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