MI                      Calculate Mutual Information
[,maiges-method         Sub-setting methods for maiges objects
activeMod               Functional classification of gene groups
activeModScoreHTML      Save HTML file with global gene scores from
                        functional gene groups classification
activeNet               Functional classification of gene networks
activeNetScoreHTML      Save HTML file with scores and p-values from
                        functional gene networks classification
addGeneGrps             Function to load gene groups into maigesPreRaw
                        object
addPaths                Function to load gene pathways into
                        maigesPreRaw object
bootstrapCor            Calculate bootstrap p-values for correlation
                        measures
bootstrapMI             Calculate bootstrap p-values for mutual
                        information (MI) measures
bootstrapT              Calculate bootstrap p-values for t statistics
boxplot                 Method boxplot for objects defined in this
                        package
calcA                   Method calcA to calculate A values
calcW                   Method calcW to calculate W values
classifyKNN             Function to do discrimination analysis
classifyKNNsc           Function to do discrimination analysis, by the
                        search and choose method
classifyLDA             Function to do discrimination analysis
classifyLDAsc           Function to do discrimination analysis, by the
                        search and choose method
classifySVM             Function to do discrimination analysis
classifySVMsc           Function to do discrimination analysis, by the
                        search and choose method
coerce,maiges,marrayNorm-method
                        Coerce a maiges object to classes defined by
                        packages limma and marray
compCorr                Compute correlation differences and their
                        p-values
contrastsFitM           Compute Contrasts from Linear Model Fit
createMaigesRaw         Function to create objects of class maigesRaw
createTDMS              Create a tab delimited file for TIGR MeV
deGenes2by2BootT        Function to do differential expression
                        analysis, comparing only two samples
deGenes2by2Ttest        Function to do differential expression
                        analysis, comparing only two samples
deGenes2by2Wilcox       Function to do differential expression
                        analysis, comparing only two samples
deGenesANOVA            Function to do differential expression
                        analysis, using ANOVA models
designANOVA             Function to construct design an contrasts
                        matrices for ANOVA models
dim.maiges              Retrieve the dimension of microarray objects
gastro                  Gastro-esophagic dataset
getLabels               Method getLabels to pick gene and sample labels
heatmapsM               Function to plot heatmaps separating groups
                        generated by SOM or k-means
hierM                   Function to do hierarchical cluster analysis
hierMde                 Function to do hierarchical cluster analysis
image                   Method image for objects defined in this
                        package
kmeansM                 Function to do k-means cluster analysis
kmeansMde               Function to do k-means cluster analysis
loadData                Load cDNA microarray data tables
maiges-class            maiges class, store normalised microarray
                        datasets
maigesANOVA-class       maigesANOVA class, extend maiges class to fit
                        ANOVA models
maigesActMod-class      maigesActMod class, store results of functional
                        classification of gene groups
maigesActNet-class      maigesActNet class, store results of functional
                        classification of gene networks
maigesClass-class       maigesClass class, store results of
                        discrimination (or classification) analysis
maigesDE-class          maigesDE class, store results of differential
                        gene expression analysis
maigesDEcluster-class   maigesDEcluster class, store results of
                        differential gene expression analysis
maigesPreRaw-class      maigesPreRaw class, store pre raw microarray
                        datasets
maigesRaw-class         maigesRaw class, store raw microarray datasets
maigesRelNetB-class     maigesRelNetB class, store results of relevance
                        network analysis (Butte's method)
maigesRelNetM-class     maigesRelNetM class, store results of relevance
                        network analysis (comparing two sample types)
normLoc                 Normalise a cDNA Microarray Object
normOLIN                Normalise a cDNA Microarray Object
normRepLoess            Bootstrap of LOWESS normalisation
normScaleLimma          Scale adjust a cDNA Microarray Object
normScaleMarray         Scale adjust a cDNA Microarray Object
plot                    Method plot for objects defined in this package
plotGenePair            Scatter plots for pair of genes
print                   Method to print a nice visualisation of the
                        objects defined in this package
relNet2TGF              Transform Relevance Network analysis in TGF
                        output
relNetworkB             Relevance Network analysis
relNetworkM             Relevance Network analysis
robustCorr              Calculate a robust correlation value
selSpots                Select spots to use in normalisation
show,maigesPreRaw-method
                        Show a nice visualisation of the objects
                        defined in this package
somM                    Function to do SOM cluster analysis
somMde                  Function to do SOM cluster analysis
summarizeReplicates     Summarise microarray objects
summary                 Method summary for the object from this package
tableClass              Save HTML or CSV tables of good classifiers
                        (cliques)
tablesDE                Save HTML or CSV tables of differentially
                        expressed genes
