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 >> >> >> > >> > >> > >> > >> > > > >