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 > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.