On 27.01.2011 05:00, Dario Strbenac wrote:
Hello,
In the documentation for agnes in the package 'cluster', it says that NAs are
allowed, and sure enough it works for a small example like :
m<- matrix(c(
1, 1, 1, 2,
1, NA, 1, 1,
1, 2, 2, 2), nrow = 3, byrow = TRUE)
agnes(m)
Call: agnes(x = m)
Agglomerative coefficient: 0.1614168
Order of objects:
[1] 1 2 3
Height (summary):
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.155 1.247 1.339 1.339 1.431 1.524
Available components:
[1] "order" "height" "ac" "merge" "diss" "call" "method" "data"
But I have a large matrix (23371 rows, 50 columns) with some NAs in it and it
runs for about a minute, then gives an error :
agnes(iMatrix)
Error in agnes(iMatrix) :
No clustering performed, NA-values in the dissimilarity matrix.
I've also tried getting rid of rows with all NAs in them, and it still gave me
the same error. Is this a bug in agnes() ? It doesn't seem to fulfil the claim
made by its documentation.
I haven't looked in the file, but you need to get rid of all NA, or in
other words, all rows that contain *any* NA values.
Uwe Ligges
The matrix I'm using can be obtained here :
http://129.94.136.7/file_dump/dario/iMatrix.obj
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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