PairComp-class          Class "PairComp" Represents the results of
                        pairwise comparison between two experimental
                        factors
QCStats-class           Class "QCStats"
all.present             Filter by PMA call
all.present.in.group    Filter by PMA call
bg.correct.sa           Simpleaffy Implementation of Mas5 Background
                        Correction
blue.white.red.cols     Generate colourings for heatmaps
call.exprs              Generate Expression Summaries for Affymetrix
                        Data
detection.p.val         Calculate Detection p-values
get.annotation          Get annotation data for a gene list
get.array.indices       Find arrays in an AffyBatch object defined by
                        their phenoData
get.array.subset        Get a subset of arrays from an affybatch
                        object, split by phnotypic data
get.array.subset.affybatch
                        Get a subset of arrays from an affybatch
                        object, split by phnotypic data
get.fold.change.and.t.test
                        Compute fold change and t-test statistics
                        between two experimental groups
hmap.eset               Draw a heatmap from an AffyBatch object
hmap.pc                 Draw a heatmap from an PairComp object
journalpng              Produce a device for producing artwork for
                        presentations and journals
justMAS                 Generate Expression calls using a C
                        implementation of the MAS 5.0 Algorithm
pairwise.comparison     Compute pairwise comparison statistics between
                        two experimental groups
pairwise.filter         Filter pairwise comparison statistics between
                        two experimental groups
plot.pairwise.comparison
                        Plots a PairComp object
plot.qc.stats           Plots a QCStats object
qc                      Generate QC stats from an AffyBatch object
qc.affy                 Generate Affymetrix Style QC Statistics
qc.get.alpha1           Get or set the alpha values for the current QC
                        environment
qc.get.array            Get or set the name of the array for which the
                        current QC environment is valid. Currently not
                        used for anything important; is a free text
                        identifier.
qc.get.probes           Retrieve QC probeset names for the current
                        array type
qc.get.ratios           Retrieve pairs of probesets used for
                        calculating 3'/5' ratios
qc.get.spikes           Retrieve QC spike probeset names for the
                        current array type
qc.have.params          Does simpleaffy have a QC definition file for
                        the specified array?
qc.ok                   Has simpleaffy's QC environment been set up?
qc.read.file            Read a file defining the QC parameters for a
                        specified array and set up the QC Environment
qcs                     an example QC Stats object
read.affy               Read a Set of .CEL Files and Phenotypic Data
read.affy.mixed         Read a Set of .CEL Files and Phenotypic Data
                        from mixed chip types
setQCEnvironment        Establish the appropriate QC environment for
                        the specified array
simpleaffy-deprecated   Does simpleaffy have a QC definition file for
                        the specified array?
standard.pearson        A clustering function based on pearson
                        correlation
trad.scatter.plot       Does a Traditional Scatter Plot of Expression
                        Data