I do think this is more of a Bioconductor question -- but no worries, they're all much nicer there than we are here and won't flame you if you double post :-)
Best, Michael On Thu, Jun 14, 2012 at 12:37 PM, Hans Thompson <hans.thomps...@gmail.com> wrote: > I know that there are quite a few packages out that there for cluster > analysis. The problem that I am facing is finding a package that will not > incorporate all my samples into clusters but just the samples that fit a > threshold (that I have not set yet and may need help finding the right > level) for genotyping. It should be able to "no call" samples outside the > clusters. It also needs to accommodate a negative control sample by not > including it in any genotype cluster. > > I'm looking at both nuclear and mitochondrial DNA so hopefully it can be > sophisticated enough to set the number of cluster between two or three > within the array. > > These genotyping arrays are either 48 samples x 48 assays, 96x96, or 192x24 > and it would be nice if it could accommodate any range of samples and > assays. > > the data headings from the csv are: > > ID,Assay,Allele Y,Allele X,Name,Type,Auto,Confidence,Final,Converted,Allele > Y,Allele X > > where Allele Y and Allele X are the plotted values and the vectors within > the data.frame are 9216 (96x96) long. > > So what would be the recommended package for moving to a more quantifiable > method of genotyping using cluster analysis? > > Thanks again. Forgive me if this is a better question for bioconductor. I > will provide any additional context that I might have forgot to add here > that could help. > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.
