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
alpha                   The alpha paramaters used to calculate PMA
                        calls
bg.correct.sa           Simpleaffy Implementation of Mas5 Background
                        Correction
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.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
getActin3               Gets the probesetid for the specified control
                        probe
getActin5               Gets the probesetid for the specified control
                        probe
getActinM               Gets the probesetid for the specified control
                        probe
getAllQCProbes          Get the names of all the QC (not spike-in)
                        probes on the array
getAllSpikeProbes       Get the names of all the Spike (not QC) probes
                        on the array
getAlpha1               Gets the probesetid for the specified control
                        probe
getAlpha2               Gets the probesetid for the specified control
                        probe
getBioB                 Gets the probesetid for the specified control
                        probe
getBioC                 Gets the probesetid for the specified control
                        probe
getBioD                 Gets the probesetid for the specified control
                        probe
getCreX                 Gets the probesetid for the specified control
                        probe
getGapdh3               Gets the probesetid for the specified control
                        probe
getGapdh5               Gets the probesetid for the specified control
                        probe
getGapdhM               Gets the probesetid for the specified control
                        probe
getQCParams-methods     Get Array Dependent QC Parameters
getTao                  Gets the probesetid for the specified control
                        probe
haveQCParams            True if data exists in the QC environment
                        describing the specified chip
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.probes               The name of the spike probes
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
spikeInProbes           Accessor Methods for QCStats class
spikes                  The name of the spike probes
trad.scatter.plot       Does a Traditional Scatter Plot of Expression
                        Data
