This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express [1] or GEO [2], or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma [3]. Enrichment scores [4] are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Significance scores are output in Cytoscape http://www.cytoscape.org/ format.
For a set of ranked gene expression profiles, enrichment scores to a default or custom set of profiles. The ranked gene expression profiles can have been generated from generate profiles or provided by the user. The enrichment scores are assessed for significance using permutations to generate random profiles.
Given a list with two elements, one containing ranklists for a set of regression models and the second containing the associated p-values. This function is used to extract a subset of the models.
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