The GeneExpressionSignature add-on is an implementation of computing distances among preprocessed gene-expression profiles of samples for R. The distances can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest, and construct connectivity map.
Merging the assay data according to phenotypic data of the input ExpressionSet. Each group of the ranked lists with the same phenotypic data is aggregated into a single list, return it as an ExpressionSet object.
Compute pairwise distances between sample according to their (Prototype Ranked List) PRL, a N x N distance matrix is generated by calling this function, N is the length of PRL.
Compute pairwise distances between sample according to their (Prototype Ranked List) PRL, get a N x N distance matrix is generated by calling this function , N is the length of PRL.
Sorting the microarray probe-set identifiers according to the differential expression values with respect to the untreated hybridization to obtaine a ranked list. Gene-expression profiles in are represented in a nonparametric fashion.
providing 
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