[R] p-values pvclust maximum distance measure

[syrvn]

Hi,

I am new to clustering and was wondering why pvclust using "maximum"
as distance measure nearly always results in p-values above 95%.

I wrote an example programme which demonstrates this effect. I
uploaded a PDF showing the results


Here is the code which produces the PDF file:

-------------------------------------------------------------------------------------
s <- matrix(runif(1600,0,1000), nrow=20)

a.res1 <- pvclust(t(s), method.hclust="complete", method.dist="euclidian",
nboot=500)
a.res2 <- pvclust(t(s), method.hclust="complete", method.dist="maximum",
nboot=500)
a.res3 <- pvclust(t(s), method.hclust="complete", method.dist="canberra",
nboot=500)
a.res4 <- pvclust(t(s), method.hclust="ward", method.dist="euclidian",
nboot=500)
a.res5 <- pvclust(t(s), method.hclust="ward", method.dist="maximum",
nboot=500)
a.res6 <- pvclust(t(s), method.hclust="ward", method.dist="canberra",
nboot=500)
a.res7 <- pvclust(t(s), method.hclust="average", method.dist="euclidian",
nboot=500)
a.res8 <- pvclust(t(s), method.hclust="average", method.dist="maximum",
nboot=500)
a.res9 <- pvclust(t(s), method.hclust="average", method.dist="canberra",
nboot=500)

s <- matrix(runif(1600,0,2), nrow=20)

b.res1 <- pvclust(t(s), method.hclust="complete", method.dist="euclidian",
nboot=500)
b.res2 <- pvclust(t(s), method.hclust="complete", method.dist="maximum",
nboot=500)
b.res3 <- pvclust(t(s), method.hclust="complete", method.dist="canberra",
nboot=500)
b.res4 <- pvclust(t(s), method.hclust="ward", method.dist="euclidian",
nboot=500)
b.res5 <- pvclust(t(s), method.hclust="ward", method.dist="maximum",
nboot=500)
b.res6 <- pvclust(t(s), method.hclust="ward", method.dist="canberra",
nboot=500)
b.res7 <- pvclust(t(s), method.hclust="average", method.dist="euclidian",
nboot=500)
b.res8 <- pvclust(t(s), method.hclust="average", method.dist="maximum",
nboot=500)
b.res9 <- pvclust(t(s), method.hclust="average", method.dist="canberra",
nboot=500)

pdf("YOUR PATH/Res.pdf", width=10, height=15)

par(mfrow=c(6,3))
plot(a.res1)
plot(a.res2)
plot(a.res3)
plot(a.res4)
plot(a.res5)
plot(a.res6)
plot(a.res7)
plot(a.res8)
plot(a.res9)

plot(b.res1)
plot(b.res2)
plot(b.res3)
plot(b.res4)
plot(b.res5)
plot(b.res6)
plot(b.res7)
plot(b.res8)
plot(b.res9)

dev.off()
--------------------------------------------------------------


Why is that???
Cheers syrvn


http://r.789695.n4.nabble.com/file/n2295594/Res.pdf Res.pdf 


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