[R] cluster samples using self organizing map in R
bgunter@4567 @end|ng |rom gm@||@com
Wed Oct 10 16:43:37 CEST 2018
the rseek.org site gives many hits for "self organizing maps", including
the som package among others.
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Tue, Oct 9, 2018 at 11:14 PM A DNA RNA <email2mrna using gmail.com> wrote:
> Dear All,
> Who can I use Self Organizing Map (SOM) results to cluster samples? I have
> tried following but this gives me only the clustering of grids, while I
> want to cluster (150) samples:
> iris.sc <- scale(iris[, 1:4])
> iris.som <- som(iris.sc, grid=somgrid(xdim = 3, ydim=3, topo="hexagonal"),
> rlen=100, alpha=c(0.05,0.01))
> ##hierarchical clustering
> groups <- 3
> iris.hc <- cutree(hclust(dist(iris.som$codes[])), groups)
> #V1 V2 V3 V4 V5 V6 V7 V8 V9
> #1 1 2 1 1 2 3 3 2
> Can anyone help me with this please?
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