Question about heatmap
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@giovanni-dario-1497
Last seen 9.6 years ago
Hello everybody I'have a general question about the heatmap function. I'm clustering an expression matrix with different dissimilarity measures. Correct if I'm wrong but if I want to cluster the columns I have to scale the rows to bring the genes to a common range, and this is apparently the default behavior of heatmap (according to the option scale="row"). So I expected to see different dendrograms, setting scale="none", but there's no change. It seems that the scaling only affects the plotting but not the generation of dendrograms. Where's the mistake? Thank you in advance Best regards Giovanni d'Ario
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@james-w-macdonald-5106
Last seen 14 hours ago
United States
Giovanni d'Ario wrote: > Hello everybody > I'have a general question about the heatmap function. I'm clustering an > expression matrix with different dissimilarity measures. Correct if I'm > wrong but if I want to cluster the columns I have to scale the rows to > bring the genes to a common range, and this is apparently the default > behavior of heatmap (according to the option scale="row"). So I expected > to see different dendrograms, setting scale="none", but there's no > change. It seems that the scaling only affects the plotting but not the > generation of dendrograms. Where's the mistake? > Thank you in advance > Best regards Although it is common to do heatmaps for microarray data, this function is part of base R so this question is better asked on the R-help list. If you take a look at the code for heatmap you can see that the scaling is done on the data after the call to hclust() - it is only there to make the color range reasonable for comparison purposes. Best, Jim > > Giovanni d'Ario > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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