>Hello again... I still have some questions. If you have the time Sean (or >someone else) I would be very grateful. > >Yes, the M-values are log, but I have checked and I do not have any >infinite or NaN values in the matrix. > >I have som questions regarding hclust. It says that the function >calculates the distances row-wise in the helpfile. But what I do not >understand is that I have chips with M-values that are seperated >column-wise. Am I supposed to have them by row instead? > >Another question. >The function looks like this hclust(as.dist(myobject), method ="complete") >The as.dist have euclidean distance by default and the hclust have >"complete" as default. What does that mean, that It calculates two?? >distances or that on distancemeasure is "shut off"? > >And the final question. >If I use hclust to create an object to use in the heatmap function, is >that the object that I give to the heatmapfunction both as colv and rowv? >heatmap(x=mymatrixwithcorrelations, Rowv = >distanceofmymatrixwithcorrelations, >Colv=distanceofmymatrixwithcorrelations, distfun=dist, hclustfun = hclust >... etc) ? > >Or is there a way to fist cluster by row in hclust and then by column? > >Thanks for the help > >/ A very confused person > > > > >>>I assume that the M values are a log, so you might check to be sure that you >>>do not have infinite or NaN results from taking logs of zero and the like. >>> >>>As for dist, use ?dist to get the help file for dist. There are other >>>distances that you can use (by changing the arguments to dist). However, >>>one trick that I have found useful is to do your clustering as you want it >>>done before calling heatmap and then call heatmap with Rowv=rowclust and >>>Colv=colclust where rowclust and colclust are "cluster" objects that you can >>>obtain from calling hclust. In this way, you can make your clusters "look >>>good" before spending the time having heatmap do it for you each time. >>> >>>Hope that helps. Oh, by the way, I am absolutely not an expert, so check >>>with other folks, also. >>> >>>Sean >>******************************************************************** *********************** >> ********************************************************************** ********************* Marcus Gry Bj?rklund Royal Institute of Technology AlbaNova University Center Stockholm Center for Physics, Astronomy and Biotechnology Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 39 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv?gen 30B