******************** Changes in EMA1.3.2 ******************** - test.LC Add the 'global' parameter to specify if one want to perform a F test of the global hypothesis H0=0, or to test each contrast simultaneously - normAffy Add the fast argument for GCRMA normalisation - ordinal.chisq Chisq test for ordinal values - New utilities intersectg setdiffg - plot.sample Allow vector as input. Transformation in matrix. - expFilter Add p parameter to keep the probes if at least p*ncol(data) of its values is higher than the threshold - clustering.plot Remove pdf option Change the margin values. Calculate the margins taking into account the names and names.sup parameters ******************** Changes in EMA1.3.1 ******************** - clust.dist.R Changes in correlation function - plotSample.R Add ellipses in the graphical output - clustering.plot.R Bug in heatmap legend Stopifnot colnames data - km Graphical options changed - clustering.plot.R lab and lab.sup can be data.frame, casting to matrix is done manually new option legend.pos allows the user to choose the legend position - genes.selection the user can specify the quantile to be computed to filter the genes ******************** Changes in EMA1.2 ******************** - Add NAMESPACE file and update DESCRIPTION file - Hide the following internals functions : clust.dist, dice, FWER.Bonf, goReport, GSA.correlate.txt, htmlresult, jaccard, keggReport, MFAreport, qualitySample - Remove the following functions : plotExplore.R, mult.clustering.R - runGSA.R Add gene scores in output - runInTest.R Update of the plot in output - runHyperGO Bug ifnotfound mget function - runHyperKEGG Bug ifnotfound mget function - normAffy Bug missing function - vignette updated ******************** Changes in EMA1.1 ******************** - runPCA.R * Bug : plotVariable option. * Label is not initialized. - clustering.plot.R * A legend is added when a label is specified * If data is specified, an heatmap is displayed in one way clustering * The margins were adjusted according to the names length * Deals with NA values in labels - bioMartAnnot.R * Bug : outputTypeId undefined - probePlots.R * Bug : cex.axis option * Add a legend - distrib.plot.R * Change display using density plot instead of histogram - sample.plot.R * Legend is displayed out of the graph - eval.stability.clustering.R * Details section is added in the man page - test.LC.R * Global parameter : if someone want to perform a F test of the global hypothesis H_0=0, or to test each contrast simultaneously * Add multiple testing correction - FDR-BH.R * Bug in the Two-stages procedure. The error rate parameter (q) is missing. - runMFA.R * Can write a pdf report or a txt report - runHyperGO * CategorySize is used to generate all the report - man pages updated - vignette updated