[BioC] Heatmap function
Liaw, Andy
andy_liaw at merck.com
Mon Nov 3 14:19:27 MET 2003
> From: Mark Reimers [mailto:Mark.Reimers at 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 Björklund
>
> Royal Institute of Technology
> AlbaNova University Center
> Stockholm Center for Physics, Astronomy and Biotechnology
> Department of Molecular Biotechnology 106 91 Stockholm, Sweden
>
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>
>
> --
> Mark Reimers
> Assistant Professor, Biosciences, and
> Statistical Lead, Bioinformatics and Expression Analysis
> Facility, Karolinska Institute Stockholm (by WebMail)
>
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