[BioC] Heatmap function

Mark Reimers Mark.Reimers at biosci.ki.se
Sun Nov 2 22:28:24 MET 2003

Hi Marcus,

You can calculate your own distances, using for example sum(
abs(data[,i]-data[,j], na.rm=T) to compute the 'Manhattan' distance
between samples i & j. If you put these into a symmetric matrix X, the R
function as.dist(X) will transform these into a distance object you can
use with hclust().



>Hmm, your answer left me thinking about how to measure distances. Why
>doesnt a distace function just calculate the distance between the values
>that are there and leave out the NA:s? I have filtered away with the
>B-test the spots that are supposedly not to be differentially expressed
>and have only a subset of the total number of spots. Three slides of my 18
>have many NA:s. Should I exclude them therefor because the distance is to
>/ Marcus
Marcus Gry Björklund

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

Phone (office): +46 8 553 783 39
Fax: + 46 8 553 784 81
Visiting adress: Roslagstullsbacken 21, Floor 3
Delivery adress: Roslagsvägen 30B

Mark Reimers
Assistant Professor, Biosciences, and
Statistical Lead, Bioinformatics and Expression Analysis Facility,
Karolinska Institute
(by WebMail)

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