Fstat                   Calculation of F statistic by gene given a
                        linear model
GSEA.mean.t             Gene Set Enrichment Analysis using output from
                        samroc
JT.test                 Jonckheere-Terpstra trend test
R2BASE                  Produces a BASE file
R2mim                   Output a script file to WinMIM
Xprep                   Fitting of a linear model
Xprep.resid             Calculation of input of residuals from linear
                        model
clin2mim                Output a script file to WinMIM, linking
                        clinical data and gene expression
cluster.q               Clustering Goodness measured by Q2
estimatep0              Estimate proportion unchanged genes
fetchSignal             Fetch data from the GATC database
firstpass               First pass description of GeneChip data
fom                     Clustering Figure of Merit
fp.fn                   Calculation of fp and fn based on a vector of
                        p-values
gap                     GAP statistic clustering figure of merit
list.experiments        Display all experiment names and id's
list.intersection.p     p-value for intersection of two gene lists.
mat2TeX                 Ouput matrix to LaTeX
myclus                  A clustering function
normalise               Normalise arrays
one.probeset.per.gene   Select the best probeset per gene
outlier                 Identify outliers in the multivariate
                        distribution
p0.mom                  Estimate proportion unchanged genes
pava                    Pooling of Adjacent Violators
pava.fdr                Estimate of the FDR and the proportion
                        unchanged genes
rank.genes              Rank genes with respect to multiple criteria
rank.trend              Trend analysis based on ranks
rsd.test                Compare two groups with respect to their RSD
                        (CV)
samroc.result-class     Class "samroc.result" for results of the
                        function samrocN
samrocN                 Calculate ROC curve based SAM statistic
samrocNboot             Calculate ROC curve based SAM statistic
union.of.pways          Create the union of two pathway lists
