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Question: How can I get Heatmap using dChip clustering..which is nice& easy to see patterns
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gravatar for michael watson IAH-C
13.9 years ago by
michael watson IAH-C3.4k wrote:
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@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 __________________________________ The all-new My Yahoo! - Get yours free! _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink modified 13.9 years ago by SAURIN1.1k • written 13.9 years ago by michael watson IAH-C3.4k
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gravatar for SAURIN
13.9 years ago by
SAURIN1.1k
SAURIN1.1k wrote:
Hi Mike, Thanks a lot, it works great now. I still have one quick question..can we display range of colors or side barrs or value on bottom of heatmap bar? thanks again, Saurin --- "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> wrote: > 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@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 > > > > __________________________________ > > The all-new My Yahoo! - Get yours free! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > __________________________________ Meet the all-new My Yahoo! - Try it today!
ADD COMMENTlink written 13.9 years ago by SAURIN1.1k
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