On this basis, a model with three lags was estimated, since it ensured that residuals were uncorrelated, saving degrees of freedom and obtaining a more parsimonious model.
An alternative is to model the batch ID as a random intercept in the regression model, saving degrees of freedom and potentially increasing power.
This procedure permits to save degrees of freedom, preserving the same accuracy of a full layer-wise description.
First, it saves degrees of freedom, and hence generally reduces the variance of the estimators of the fixed effects, and second, some variance parameters can be estimated, which in the case of our model are more relevant descriptors of the biological phenomena.
Conditioning on cluster is often done with random effects to save degrees of freedom.
In this setting the GCA model is at a distinct advantage: it knows a priori the true architecture and can thus save degrees of freedom from fitting specious parameters.
First, the Laplacian matrix was calculated as L = D − W, where D was a diagonal matrix saving the degree of each node (i.e., the row sum).
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