[R] agnes clustering and NAs

Dario Strbenac D.Strbenac at garvan.org.au
Thu Jan 27 05:00:10 CET 2011


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.

The matrix I'm using can be obtained here :

Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

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