Hi, Try allt.som$visual Edgar Acuna UPRM On Thu, 9 Jun 2005, Ken Termiso wrote:
> Hi all, > > I originally posted this to the bioconductor group, but maybe it's better > suited to the r-help... > > I'm using som() to partition samples of gene expression data into clusters. > The point is to classify control vs. experimental cases (sample clustering). > The original matrix was 22283 x 8. The 8 samples have 4 controls and 4 > experimentals. > > I transposed the matrix so that its dim are 8 x 22283, and called that > "allt." Using the normalize() function from som library, I scaled the data > to have mean zero and variance 1. > > allt.som <- som(allt, xdim=5, ydim=5, topol="hexa", neigh="bubble", alpha=1) > plot(allt.som) > > What I cannot figure out how to do is how to determine where each sample has > clustered, since the plot that i'm using does not include labels...I also > tried str(allt.som) but cannot determine which attribute calls where each > sample has gone...all I would like to know is where samples are being placed > in the SOM grids, to make sure that the controls cluster together and exps > cluster together. (Also I would eventually like to cluster the genes with > SOM and also like to know which genes are clustered in which grids, which is > the same problem as I have with the samples). > > Thanks in advance, > Ken > > > >str(allt.som) > List of 16 > $ data : num [1:8, 1:22277] 1167 1282 1561 1398 1581 ... > ..- attr(*, "dimnames")=List of 2 > .. ..$ : chr [1:8] "m577con" "m577exp" "m578con" "m578exp" ... > .. ..$ : chr [1:22277] "1007_s_at" "1053_at" "117_at" "121_at" ... > $ code : matrix [1:25, 1:22277] 1050 1222 1411 1504 1722 ... > ..- attr(*, "class")= chr "matrix" > $ visual :`data.frame': 8 obs. of 3 variables: > ..$ x : num [1:8] 0 1 3 2 3 4 2 1 > ..$ y : num [1:8] 1 2 0 1 3 3 2 4 > ..$ qerror: num [1:8] 6472 8396 7574 7856 6969 ... > $ qerror : num 6e+08 > $ init : chr "linear" > $ alpha : chr "inverse" > $ neigh : chr "bubble" > $ topol : chr "hexa" > $ alpha0 : num [1:2] 1 0.5 > $ radius0 : num [1:2] 5 3 > $ rlen : num [1:2] 16 80 > $ xdim : num 5 > $ ydim : num 5 > $ err.radius: num 1 > $ inv.alp.c : num [1:2] 0.16 0.8 > $ code.sum :`data.frame': 25 obs. of 3 variables: > ..$ x : num [1:25] 0 1 2 3 4 0 1 2 3 4 ... > ..$ y : num [1:25] 0 0 0 0 0 1 1 1 1 1 ... > ..$ nobs: int [1:25] 0 0 0 1 0 1 0 1 0 0 ... > - attr(*, "class")= chr "som" > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
