EMA-package             EMA - Easy Microarray Analysis
PLS                     Partial Least Squares
as.colors               Convert labels to colors
bioMartAnnot            Annotation of probesets using biomaRt
clustering              Agglomerative hierarchical clustering
clustering.kmeans       Kmeans and hierarchical clustering
clustering.plot         Clustering plots for one or two ways
                        representation
distrib.plot            Distribution plots of genes expression level
eval.stability.clustering
                        Compares several clustering methods by means of
                        its stability.
expFilter               Filter expression data
foldchange              Compute foldchange
genes.selection         Genes selection
intersectg              Generalized version of intersect for n objects
km                      Compute survival curves and test difference
                        between the curves
makeAllContrasts        Create all pairwise contrasts
marty                   marty data
marty.type.cl           marty class data for Basal vs HER2 cancer type
multiple.correction     Multiple testing correction
myPalette               Microarray color palette
normAffy                Normalisation of Affymetrix expression arrays
ordinal.chisq           Chisq test for ordinal values
plotBiplot              Sample and variable representation on a same
                        graph for PCA
plotInertia             Barplot of component inertia percentage for PCA
plotSample              Sample representation for Principal Component
                        Analysis
plotVariable            Variable representation for Principal Component
                        Analysis
probePlots              Plot the expression profiles of the probes
                        corresponding to given probesets
runGSA                  GSA analysis
runHyperGO              Run Gene Ontology analysis based on
                        hypergeometric test from a probeset list
runHyperKEGG            Run KEGG pathway analysis based on
                        hypergeometric test from a probeset list
runIndTest              Computing Differential Analysis for each gene
runMFA                  Function to perform a Multiple Factor Analysis.
runPCA                  Perform an Principal Component Analysis
runSAM                  SAM analysis with siggenes package
runTtest                Computing Multiple Student Tests
runWilcox               Computing Multiple Wilcoxon Tests
sample.plot             barplot of genes expression level
setdiffg                Generalized version of setdiff for n objects
test.LC                 Test linear combinations of parameters of a
                        linear model
test.nested.model       Test for nested ANOVA models
