Article ID: 209 - Last Modified: December 4, 2010
When using Canvas Diversity Analysis, how big of a subset can I select, and how do I choose the value of the exclusion sphere size ?
When performing Diversity Analysis on a large data set, we recommend sphere exclusion ("sphere") or directed sphere exclusion ("dise") as the diversity selection method. These methods do not store the matrix of similarities or distances. The memory scales linearly with the size of the full data set.
On the other hand, the computational expense is quadratic with respect to the subset size. So the subset should be kept reasonably small. We recommend that the subset remain below the square root of the number of compounds in the full data set.
To determine the exclusion sphere size that will result in such a subset, we suggest that you select a subset of the total pool, and experiment to find a suitable value of the sphere size. A subset of size sqrt(N) is good for this exercise.
Keywords: Canvas, DBCS, diversity analysis, exclusion sphere
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