1.4.1 o plot1gene now coerces the 'groups' variable to a factor in plot1gene 1.4.0 o release for BioC 2.10 1.2.4 o throw error in case 'group' variable contains missing values in spectalMap 1.2.3 o circumvent build issues on certain versions of windows 1.2.2 o more appropriate handling of the dots argument in plot1gene 1.2.1 o fix in legend for spectralMap 1.2.0 o release for BioC 2.9 1.1.4 o fix in limmaTwoLevels 1.1.3 o update for revised glmnet package 1.1.1 o on BioConductor 0.0-26 o better argument handling for mpm 0.0-25 o fix histPvalue for limma objects o add histPvalue method for MArrayLM objects 0.0-24 o add proper support for the main argument in histPvalue methods. 0.0-23 o add support for cex, cex.lab, cex.main to plot1gene 0.0-22 o allow for specifying xlab and ylab in histPvalue 0.0-21 o move annotationTable tests to the a4Reporting package o complete documentation for histpvalue plotter o added heatmap.expressionSet o fix legend for spectralMap 0.0-20 o topTable method for limma objects gains default setting for n (n=10) and looses default for coef (in order to force people to make the right choice instead of the previous default of 2) o removed nlcv dependency to speed up loading a4 o remove RColorBrewer dependency (speed up loading) o changed column names of featureData to be concordant with BioConductor nomenclature o split off a4Core, a4Preproc and a4Classif packages and become a4Base 0.0-19 o move $SRC_PKG/etc to $SRC_PKG/inst/etc as tooltip.script (plotLogRatio) needs to be available at $INSTALLED_PKG/etc 0.0-18 o add varEqual argument to tTest (defaults to FALSE) o improved y axis annotation for volcanoPlot 0.0-17 o remove confusionMatrix generic as it is defined already in nlcv; otherwise the one in nlcv is masked 0.0-16 o fix colors of groups in spectralMap (now uses a4palette) o redefine topTable method for MArrayLM objects (is overwritten in nlcv) o add gene argument (as alternative to probeset) for plot1gene function o add default pointLabels in case pointLabels for volcanoPlot and its numeric,numeric,missing-method 0.0-15 o fix plot1gene (respect order of factor levels in phenoData of ExpressionSet) 0.0-14 o bug in volcanoPlot (lods values should be sorted in increasing order, contrary to P values) o add probe2gene argument to plot1gene o add topTable method for tTest objects o set default sub for spectralMap to sub="" o fix pamClass and corresponding topTable (silence it) o added xtable for topTable of pamClass o add nlcvTT data to package o expose a4palette function to user and document o add histPvalue for limmaResult object o turned propDEgenes into generic o expose volcanoplotter to user and document o add probe2gene argument to tTest, pamClass, rfClass (defaults to TRUE) o significant improvements to documentation 0.0-13 o fix seemingly inverted logic of topPValues and topLogRatios in volcanoPlot o reduce space between left 'wing' of volcanoPlot and y axis o extended volcanoPlot documentation o integrate annotationTable package into a4 o improve topTable for rfClass and fix xtable method accordingly o adapt rfClass to improved varSelRF 0.7-1 which now has a verbose=FALSE option that also silences gc() output (patches Tobias Verbeke) o add documentation for topTable methods o fix typo print.topTablePam 0.0-12 o volcanoPlot made generic, methods for 'limma', 'tTest' and numeric vectors 'x' and 'y' 0.0-11 o add varSelRF wrapper rfClass o add new addGeneInfo function to produce ExpressionSet objects similar to the pipeline o topTable method (and corresponding print and xtable methods) for lasso models o topTable method (and corresponding print and xtable methods) for rfClass models o topTable method (and corresponding print and xtable methods) for pamClass models 0.0-10 o add lassoClass o extract probe2gene function out of spectralMap.R into probe2gene.R o improve display of sample names in spectralMap 0.0-9 o fix pamr error handling mess o documentation fix in spectralMap o added mpm.args argument to set arguments for mpm (rationale: allow for PCA) 0.0-8 o fixed volcanoPlot (used two devices) 0.0-7 o split up again into separate nlcv and a4 packages 0.0-6 o updated vignettes 0.0-5 o merged nlcv 0.1-72 into the a4 package 0.0-4 o added limmaTwoGroups function o removed dependency on nlcv (to avoid circular dependencies) 0.0-3 o insert (basic) vignette on comparison of two groups o fix new page (grid) for volcanoPlot o improved y-axis annotation for volcanoPlot o add probe2gene argument to spectralMap for alternative labeling of points (needs mpm >= 1.0-10) o added name space to hide probe2gene function o explicited makeLognormal argument for spectralMap o changed selection of points to label in volcanoPlot (union of topPvalues and topLogRatios) 0.0-2 o spectralMap added 0.0-1 o volcanoPlot added