| Function | Description |
| 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 |
| 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 |
| 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 |
| 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 |
| get.fold.change.and.t.test | Compute fold change and t-test statistics between two experimental groups |
| 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 |
| PairComp-class | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| 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 QC probes |
| QCStats-class | Class "QCStats" |
| 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 |