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
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