1.5.2 o remove require(mouse4302mmentrezg.db) calls to keep R CMD check from giving inappropriate warnings 1.5.0 o update exampleGeneSet.rda using GO.db for BioC 2.11 1.4.2 o further improvements in getGeneSets and addGeneSetDescription 1.4.1 o better checks on geneSetSource in getGeneSets 1.3.0 o update using new annotation packages o move to roxygen2 1.2.1 o also export addGeneSetDescription 1.2.0 o BioC release 2.9 1.1.1 o update using new annotation packages o apply changes to column permutations (contributed by Heather Turner) 0.99.5 o further adaptations for use with the reactome.db package 0.99.4 o adapt MLP for use with the reactome.db package (Willem Ligtenberg) 0.99.3 o fix mlpBarplot (p values equal to 0) reported and patched by Willem Ligtenberg 0.99.2 o fix bug in plotGeneSetSignificance (barColors argument) 0.99.1 o fix mouse4302.db dependency of vignette 0.99.0 o no longer export utility functions 0.0-14 o add examples to help pages 0.0-13 o comply with R 2.12.x 0.0-12 o fix main title handling in plotGOgraph o fix main title handling for mlpBarplot in case the geneSetSource are external data (data frame) 0.0-11 o fix in plotGeneSetSignificance (psids) o typo NEWS file 0.0-10 o updated vignette o change argument criticalValues of the MLP function to probabilityVector o trivial change example data set 0.0-9 o updated default grey scales for plot(., type = "barplot") o default grey for plotGeneSetSignificance set to 'grey50' o substantial improvement to vignette (An) o uniform use of 'main' argument for main titles in plot functions 0.0-8 o add Dog species funcionality to getGeneSets (public GO and KEGG annotation only) o getGeneSets: replace eset argument by entrezIdentifiers argument o use geneSetSource instead of pathwaySource for uniformity across all functions (most notably getGeneSets) o plot(., type = "barplot") now allows for specifying colors for the bars (barColors argument) and includes fix o fix colors and legend for plot(., type = "GOgraph") o added plotGeneSetSignificance o impose character type for geneSetDescription in MLP output (instead of factor) 0.0-7 o add type = "GOgraph" to the plot method for MLP objects o rudimentary draft for vignette included 0.0-6 o store pathwaySource information in MLP output object o integrate addGeneSetDescription into MLP function and adapt mlpBarplot accordingly o remove plot argument from quantileCurves (argument was not used) o introduce plot method with support for type = "barplot" and type = "quantileCurves" 0.0-5 o goAnnotation replaced by the more general getGeneSets (for other pathway sources than the GO data base) o added mlpBarplot 0.0-4 o significant speedups for goAnnotation and addGeneSetDescription o renamed summary.MLP to addGeneSetDescription o add support for dogs o documentation fixes o remove (deprecated) goInputMLP o remove dead code in goAnnotation o remove pperm, tStatistic and their utility functions (limma being preferred) 0.0-3 o fix probeset names (exclude non-numeric ones) 0.0-2 o fix in summary.MLP 0.0-1 o first package version