# self-organizing map in R

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This is my first SOM figure 🙂

Thanks to the som package and example code from Jun Yan. Here is my code for the figure:

require(som)

rpkm <- Tx_rpkm[, -c(1:4)]

rpkm.f <- filtering(rpkm, lt=10, ut=30000, mmr=2, mmd=10)

# rpkm.f=log(rpkm.f+0.1) # this doesn’t really change much of the result

rpkm.f.n <- normalize(rpkm.f)

foo <- som(rpkm.f.n, xdim=5, ydim=5, topol="rect", neigh="bubble")

png(“../results/clustering.SOM.RNAseq.png”,width=800, height=800)

plot(foo,yadj=0.15, main=”Expression profiles obtained by self-organizing map (SOM) clustering \nof individual mRNA transcript throughout the time-course”, xlab=”Stage: D13 – D14 – D15 – D16 – D17 – D18″)

dev.off()

I am still not very clear how to choose the proper xdim and ydim. Also, what’s the color code for the bar mean? Hope anyone know SOM could leave comment here. Or, I will read article myself 🙂

Is the normalization necessary?

To

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