[R] Calculating the distance samples using distance metics method
Keizer_71
christophe.lo at gmail.com
Wed Feb 20 00:34:33 CET 2008
***********reading in data**********
data<-read.table("microarray.txt",header=T, sep="\t")
head(data)
dim(data)
attach(data)
***********creating matrix and calculating variance across probesets********
x<-1:20000
y<-2:141
data.matrix<-data.matrix(data[,y])
variableprobe<-apply(data.matrix[x,],1,var)
hist(variableprobe)
**************filter out low variance*************
data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,]
dim(data.sub)
[1] 10000 140
What is the best way to calculate the distances between the samples using
the euclidean or manhattan distance metrics?
any suggestions?
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