Robert Gentleman

TL;DR: Two key aspects of the Connectivity Map implementation are revisited, including new approaches to measuring closeness for the common scenario wherein the query constitutes an ordered list and an alternate inferential approach based on generating empirical null distributions that exploit the scope, and capture dependencies, embodied by the database.

TL;DR: The proposed solution to the development of standards in systems-biology research is presented as a ‘top-down’ approach that ignores many existing and emerging standards and seems based on false assumptions about the research community and ignores the community it is intended to serve.

TL;DR: A Bayesian error‐in‐variable model is described for the analysis of microarray data from a clinical study of patients with acute lymphoblastic leukemia, focusing in particular on the problem of identifying genes whose expression patterns are associated with duration of remission.

TL;DR: In the example reported by Talloen et al. (1), the detection power achieved by the more general—and thus, more broadly applicable—overall variance filter was as good as or better than that of a technology-specific criterion at all filtering thresholds.

TL;DR: This article proposes controlling the positive FDR using a Bayesian approach where the rejection rule is based on the posterior probabilities of the null hypotheses, and illustrates the procedure with an application to wavelet thresholding.