[BioC] How can I get Heatmap using dChip clustering..which is nice& easy to see patterns

[michael watson (IAH-C)]

Hi Saurin

I may be wrong, but it looks like your code calculates the euclidean
distance between rows of 1-cor(), which is itself a distance matrix of
sorts.  Try:

row.dist <- as.dist(1 - cor(t(esetSub2X)))
col.dist <- as.dist(1 - cor(esetSub2X))
heatmap(esetSub2X, Colv=as.dendrogram(hclust(col.dist,
method="average")), Rowv=as.dendrogram(hclust(row.dist,
method="average")))

Mick

-----Original Message-----
From: Saurin Jani [mailto:saurin_jani at yahoo.com] 
Sent: 15 November 2004 23:28
To: Bioconductor Bioconductor
Subject: [BioC] How can I get Heatmap using dChip clustering..which is
nice& easy to see patterns


Hi ,

How can I get dChip clustering on heatmap?..which is
nice & easy to see patterns.

I am using 1- cor(eset)  but somehow its not working I
am still getting diff. kind of clustering dendrogram.

> d <- dist((1 - cor(esetSub2X)),method =
"euclidean");
> dCol <- dist(t((1- cor(esetSub2X))),method =
"euclidean");

> heatmap(esetSub2X,Colv=
as.dendrogram(hclust(d,method = "complete")),Rowv =
NA,col = rbg,cexRow = 1,cexCol = 1);


Am I missing something?

Any heatmap clustering  is helpful.

Thank you,
Saurin


		
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