PairComp-class          Class "PairComp" Represents the results of
                        pairwise comparison between two experimental
                        factors
QCStats-class           Class "QCStats"
bg.correct.sa           Simpleaffy Implementation of Mas5 Background
                        Correction
bioB                    Accessor Methods for QCStats class
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
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
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.qc.stats           Plots a QCStats object
qc                      Generate QC stats from an AffyBatch object
qc.affy                 Generate Affymetrix Style QC Statistics
read.affy               Read a Set of .CEL Files and Phenotypic Data
trad.scatter.plot       Does a Traditional Scatter Plot of Expression
                        Data
