Abstract
Exploratory analysis is an important first step for discovering latent struc-
ture and generating hypotheses in large biological data sets. However, when
the number of variables is large compared to the number of samples, standard
methods such as principal components analysis give results that are unstable
and difficult to interpret.
Here, we present adaptive generalized principal components analysis
(adaptive gPCA), a new method that solves these problems by incorporat-
ing information about the relationships among the variables. Adaptive gPCA
gives a low-dimensional representation of the samples with axes that are inter-
pretable in terms of groups of closely related variables. We show that adaptive
gPCA does well at reconstructing true latent structure in simulated data and
demonstrate its use on a study of the effect of antibiotics on the human gut
microbiota.
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