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(). regards Mark >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 >affected? > >/ Marcus > > ********************************************************************** ********************* Marcus Gry Bj?rklund 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: Roslagsv?gen 30B -- Mark Reimers Assistant Professor, Biosciences, and Statistical Lead, Bioinformatics and Expression Analysis Facility, Karolinska Institute Stockholm (by WebMail)

> From: Mark Reimers [mailto:Mark.Reimers@biosci.ki.se] > > 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(). But this effectively treats components containing NAs as contributing 0 to the distance. Is that really a reasonable thing to do? As an example: point #1: 3, 7, NA, 6, 1 point #2: 5, NA, 1, 8, 0 Ignoring the NAs gives dist(1, 2) = |3-5| + |6-8| + |1-0|, which is the same as having: point #1: 3, 7, 1, 6, 1 point #2: 5, 7, 1, 8, 0 Is that really what you want? Andy > regards > > Mark > > >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 affected? > > > >/ Marcus > > > > > ************************************************************** > ***************************** > Marcus Gry Bj?rklund > > 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: Roslagsv?gen 30B > > > > -- > Mark Reimers > Assistant Professor, Biosciences, and > Statistical Lead, Bioinformatics and Expression Analysis > Facility, Karolinska Institute Stockholm (by WebMail) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo> /bioconductor >