agnes clustering and NAs
On Thu, 2011-01-27 at 10:45 +0100, Uwe Ligges wrote:
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.
If one believes the documentation, then that only applies to the case where `x` is a dissimilarity matrix. `NA`s are allowed if x is the raw data matrix or data frame. The only way the OP could have gotten that error with the call shown is if iMatrix were not a dissimilarity matrix inheriting from class "dist", so `NA`s should be allowed. My guess would be that the OP didn't get rid of all the `NA`s. Dario: what does: sapply(iMatrix, function(x) any(is.na(x))) or if iMatrix is a matrix: apply(iMatrix, 2, function(x) any(is.na(x))) say? G
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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