DEMICel                 Creates a 'DEMICel' object
DEMICel-class           Class 'DEMICel'
DEMIClust               Creates a 'DEMIClust' object
DEMIClust-class         Class 'DEMIClust'
DEMIDiff                Creates a 'DEMIDiff' object
DEMIDiff-class          Class 'DEMIDiff'
DEMIExperiment          Creates a 'DEMIExperiment' object
DEMIExperiment-class    Class 'DEMIExperiment'
DEMIGroup               Creates a 'DEMIGroup' object
DEMIGroup-class         Class 'DEMIGroup'
DEMIMessages            A 'list' of DEMI messages
DEMIPathway             Functional annotation of DEMI results
DEMIResult-class        Class 'DEMIResult'
addCustomTargets        Add new alignments to the alignment table
addCytoband             Add karyotype information to DEMI differential
                        expression results
adjust4maxprobes        Adjust the DEMI analysis by 'maxprobes'
                        analysis
attachResult            Attach results from 'DEMIDiff' object to
                        'DEMIExperiment' object
calcHypergeoExon        Calculates hypergeometric probability in DEMI
                        analysis
calcHypergeoProb        Calculates hypergeometric probability in DEMI
                        analysis
celMatrixNormalize      Initializes the normalization of the raw
                        expression matrix
check4probe             Checks if the probes are available
check4target            Checks if the targets are available
checkDEMIExperiment_analysis
                        Checks if the 'analysis' is correct
checkDEMIExperiment_celpath
                        Checks if 'celpath' is correct
checkDEMIExperiment_experiment
                        Checks if the 'experiment' is correct
checkDEMIExperiment_maxprobes
                        Checks if 'maxprobes' is correct
checkDEMIExperiment_maxtargets
                        Checks if 'maxtargets' is correct
checkDEMIExperiment_normalization
                        Checks if 'normormalization' is correct
checkDEMIExperiment_pmsize
                        Checks if 'pmsize' is correct
cleanorganismname       Cleans the organism name from redundant
                        characters
cluster                 Initializes the clustering of probes into
                        clusters
createGroup             Creates a 'DEMIGroup' object
customObject            Checks if the 'DEMIClust' object is user
                        defined or automatically generated
demi                    A wrapper for DEMI analysis
demi.comp.test          Cluster probes into higher and lower clusters
                        based on their differential signalling
demi.t.test             Cluster probes into higher and lower clusters
                        based on their differential signalling
demi.wilcox.test        Cluster probes into higher and lower clusters
                        based on their differential signalling
demi.wilcox.test.fast   Cluster probes into higher and lower clusters
                        based on their differential signalling
demiequal               Cluster probes that have no statistically
                        significant differential signalling
demisummary             Returns the mean normalized expression levels
                        for the specified targets
diffSpliceScore         Calculate differential splice scores
diffexp                 Initializes the differential expression
                        analysis
findCytoband            Finds cytoband for the specified genome region
getAlignment            Returns the 'blatTable' parameter representing
                        alignment information
getAnalysis             Returns the 'analysis' parameter
getAnnotation           Returns the 'annoTable' parameter representing
                        annotation information
getArraytype            Returns the 'arraytype' parameter
getCelMatrix            Returns the raw expression matrix
getCelpath              Returns the 'celpath' parameter
getClustMethod          Returns the 'clust.method' parameter
getCluster              Returns the 'cluster' parameter
getCutoffPvalue         Returns the 'cutoff.pvalue' parameter
getCytoband             Returns the 'cytoband' parameter representing
                        karyotype information
getDEMIClust            Returns the 'cluster' parameter
getExperiment           Returns the 'experiment' parameter
getGroup                Returns the 'group' parameter
getGroupA               Returns the 'groupA' parameter
getGroupB               Returns the 'groupB' parameter
getGroupNames           Returns the 'groupNames' parameter
getIndexA               Returns the 'indexA' parameter
getIndexB               Returns the 'indexB' parameter
getMaxprobes            Returns the 'maxprobes' parameter
getMaxtargets           Returns the 'maxtargets' parameter
getName                 Returns the 'name' parameter
getNormMatrix           Returns the normalized expression matrix
getOrganism             Returns the 'organism' parameter
getPathway              Returns the 'pathway' parameter representing
                        functional annotation information
getProbeLevel           Returns the probe levels from the normalized
                        expression matrix for the specified probes
getResult               Returns the 'result' parameter
getResultTable          Retruns the DEMI analysis results as a
                        'data.frame'
getTargetAnnotation     Returns annotation information for the
                        specified targets
getTargetProbes         Returns the probe ID's of the specified targets
initialize.DEMICel      Initializes a 'DEMICel' object
initialize.DEMIClust    Initializes the 'DEMIClust' object
initialize.DEMIDiff     Initializes the 'DEMIDiff' object
initialize.DEMIExperiment
                        Initializes the 'DEMIExperiment' object
initialize.DEMIGroup    Initializes the 'DEMIGroup' object
initialize.DEMIResult   Initializes the 'DEMIResult' object
loadAnnotation          Loads the annotation information specified by
                        the 'DEMIExperiment' object
loadBlat                Loads the alignment information specified by
                        the 'DEMIExperiment' object
loadCel                 Loads the raw expression matrix into a
                        'DEMIExperiment' object
loadCytoband            Loads the karyotype information specified by
                        the 'DEMIExperiment' object
loadDEMILibrary         Loads the DEMI annotation package specified by
                        the 'DEMIExperiment' object
loadPathway             Loads the pathway information specified by the
                        'DEMIExperiment' object
makeDEMIResultsTable    Returns a 'data.frame' of the differential
                        expression results
makeUCSCLink            Make UCSC link
matchExonGene           Matches exons to their corresponding
                        transcripts.
norm.quantile           Quantile normalization function
norm.rrank              Relative rank normalization function
probe.levels            Draws a histogram of the normalized expression
                        levels of the specified targets
probe.plot              Draws a plot of the normalized expression
                        levels of the specified targets
totalMatches_all        Calculates the number of matches over all
                        probes
totalMatches_cluster    Calculates the number of matches in the cluster
validDEMIClust          Validates the 'DEMIClust' object
validDEMIExperiment     Validates the 'DEMIExperiment' object
wprob                   Calculates wilcoxon's upper and lower
                        probabilities
