Dear List, I have another question to bother you about how to do clustering. My data consists of 49 columns (49 variables) and 238804 rows. I would like to do hierarchical clustering (unsupervised clustering and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/*pvclust* /) but I always had the problem like for R like "cannot allocate the memory". I am curious about what else packages can perform the clustering analysis while memory efficient. Meanwhile, is there any way that I can extract the features of each cluster. In other words, I would like to identify which are responsible for classifying these variables (samples). Thanks a lot! Sincerely, Alex [[alternative HTML version deleted]]
Hi Alex, just in case you're trying to get genotypes from the Affymetrix 500K set, you might want to check the oligo package available on BioConductor. best, b On Jun 7, 2007, at 10:42 PM, ssls sddd wrote:> Dear List, > > I have another question to bother you about how to do clustering. > My data consists of 49 columns (49 variables) and 238804 rows. > I would like to do hierarchical clustering (unsupervised clustering > and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/ > *pvclust* > /) > but I always had the problem like for R like "cannot allocate the > memory". > > I am curious about what else packages can perform the clustering > analysis > while memory efficient. > > Meanwhile, is there any way that I can extract the features of each > cluster. > > In other words, I would like to identify which are responsible for > classifying these > variables (samples). > > Thanks a lot! > > Sincerely, > > Alex > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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.
sorry, I hit send before finishing my thoughts... and as for clustering microarray data, you might want to consider the bioconductor mailing list... bioconductor at stat.math.ethz.ch b On Jun 7, 2007, at 10:42 PM, ssls sddd wrote:> Dear List, > > I have another question to bother you about how to do clustering. > My data consists of 49 columns (49 variables) and 238804 rows. > I would like to do hierarchical clustering (unsupervised clustering > and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/ > *pvclust* > /) > but I always had the problem like for R like "cannot allocate the > memory". > > I am curious about what else packages can perform the clustering > analysis > while memory efficient. > > Meanwhile, is there any way that I can extract the features of each > cluster. > > In other words, I would like to identify which are responsible for > classifying these > variables (samples). > > Thanks a lot! > > Sincerely, > > Alex > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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.