Joshua, I'm not sure I understand your aim correctly, but if I do, here's my advice: If you are able to find the clusters according to rows or columns using clustering, you must be using some kind of a distance matrix that encodes whether two antibodies should be in one bin for rows, and a similar matrix for the columns. To get a clustering that represents only bins that occur in both directions, you can appropriately combine the two matrices into a single matrix. For example, if the distance matrix is zero if the antibodies go together and 1 otherwise, you can add the two matrices into a single matrix, then cluster the antibodies using the combined matrix using hclust (with complete linkage, if I understand it correctly), then use cutree() with cut height equal say 0.5.
HTH, Peter On Sun, Sep 15, 2013 at 11:33 PM, Joshua Eckman <josheck...@hotmail.com> wrote: > I am working with protein blocking assays and the end result is a 2D matrix > describing which antibodies block the binding of other antibodies to the > target antigen.I need to group the antibodies together into "bins" based on > their combined profiles in both the row and column direction.I am able to > group the blocking profiles of rows vs rows, or columns vs columns, using > clustering. The end results could look something like this: >>col_bins binAb1 1Ab2 2Ab3 2Ab4 2Ab5 3Ab6 4Ab7 5Ab8 >>5Ab9 6 > In this case the "bin" values are just to describe they have similar blocking > profiles - so Ab2, Ab3, Ab4 have the same blocking profile, as do Ab7 and Ab8. > Looking at the row profiles >>row_bins binAb1 1Ab2 2Ab3 3Ab4 3Ab5 4Ab6 5Ab7 5 Ab8 >>6Ab10 7 > The important end result, where I am stuck, is how to combine this with the > row direction and only report those that are represented in both directions > AND group together in both directions. It is possible that some Abs will not > be represented in both directions. The "bin" values of row_bins and col_bins > are also not important, just the relationship between Abs by name that belong > in the same bin, in both directions. > In other words, a combined bins report would look something like this: > binAb1 A Ab3 BAb4 BAb5 C > I made this visually because it is clear that these are the only groupings > that are maintained in both directions. But real data sets are much bigger, > so I need some form of automation. > Any ideas on how do this with matrix, dendograms or clustering functions? > Thank you, > josh > > > [[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.
