[R] Help with SOM clustering package

From: Nayeem Quayum <nayeemquayum_at_gmail.com>
Date: Sat 22 Oct 2005 - 06:58:27 EST


Hello everybody,

I am trying to use SOM package to cluster some gene expression data and there fore requesting you some help. I would really appreciate if you cold help me out.

Q1. I clustered the data using SOM function and plotted it using plot function. But I can't figure out how I can list the data elements belongs to different cluster. I made a 5X5 SOM grid and there are 25 clusters. The plot tells me how many data elements belongs to this different cluster grid but I want to make separate list of them. I don't know how to deal with the SOM.object frankly speaking.

Q2. The SOM package listed 5 functions

som.init

som

som.train

som.update and

som.project

I was wondering to get the best result in what order I should apply them? Should I first initialize the som using som.init, then train it with som.train and finally update it with som.update? Or just use som function followed by som.update? As I have only one set of data I don't think I need to use project function.

Thanks in advance and regards.

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