Dissecting random and systematic differences between noisy composite data sets

Composite data sets measured on different objects are usually affected by random errors, but may also be influenced by systematic (genuine) differences in the objects themselves, or the experimental conditions. If the individual measurements forming each data set are quantitative and approximately normally distributed, a correlation coefficient is often used to compare data sets. However, the relations between data sets are not obvious from the matrix of pairwise correlations since the numerical value of the correlation coefficient is lowered by both random and systematic differences between the data sets. This work presents a multidimensional scaling analysis of the pairwise correlation coefficients which places data sets into a unit sphere within low-dimensional space, at a position given by their CC* values [as defined by Karplus & Diederichs (2012 ▸), Science, 336, 1030–1033] in the radial direction and by their systematic differences in one or more angular directions. This dimensionality reduction can not only be used for classification purposes, but also to derive data-set relations on a continuous scale. Projecting the arrangement of data sets onto the subspace spanned by systematic differences (the surface of a unit sphere) allows, irrespective of the random-error levels, the identification of clusters of closely related data sets. The method gains power with increasing numbers of data sets. It is illustrated with an example from low signal-to-noise ratio image processing, and an application in macromolecular crystallography is shown, but the approach is completely general and thus should be widely applicable.