| Function | Description |
| AffyBatch-class | Class AffyBatch |
| affybatch.example | AffyBatch instance affybatch.example |
| affy-options | Options for the affy package |
| AffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
| affy.scalevalue.exprSet | Scale normalization for expreSets |
| barplot.ProbeSet | show a ProbeSet as barplots |
| bg.adjust | Background ajustment (internal function) |
| bg.correct | Background Correction |
| cdfenv.example | Example cdfenv |
| cdfFromBioC | Functions to obtain CDF files |
| cleancdfname | Clean Affymetrix's CDF name |
| debug.affy123 | Debugging Flag |
| expresso | From raw probe intensities to expression values |
| expressoWidget | A widget for users to pick correction methods |
| fit.li.wong | Fit Li and Wong Model to a Probe Set |
| generateExprSet-methods | generate a set of expression values |
| generateExprVal | Compute a summary expression value from the probes intensities |
| generateExprVal.method.avgdiff | Generate an expression value from the probes informations |
| generateExprVal.method.playerout | Generate an expression value from the probes informations |
| hlog | Hybrid Log |
| justRMA | Read CEL files into an AffyBatch |
| list.celfiles | List the Cel Files in a Directory/Folder |
| loess.normalize | Normalize arrays |
| MAplot | Relative M vs. A plots |
| mas5 | MAS 5.0 expression measure |
| mas5calls | MAS 5.0 Absolute Detection |
| merge.AffyBatch | merge two AffyBatch objects |
| mva.pairs | M vs. A Matrix |
| normalize | Normalize - generic |
| normalize.AffyBatch | Normalize Affymetrix Probe Level Data - methods |
| normalize.constant | Scale probe intensities |
| normalize.contrasts | Normalize intensities using the contrasts method |
| normalize.invariantset | Invariante Set normalization |
| normalize.loess | Scale microarray data |
| normalize.qspline | Normalize arrays |
| normalize.quantiles | Quantile Normalization |
| normalize.quantiles.robust | Robust Quantile Normalization |
| pairs.AffyBatch | plot intensities using 'pairs' |
| plotDensity | Plot Densities |
| plotLocation | Plot a location on a cel image |
| plot.ProbeSet | plot a probe set |
| pmcorrect | PM Correction |
| ppsetApply | Apply a function over the ProbeSets in an AffyBatch |
| probeMatch-methods | Methods for accessing perfect matches and mismatches |
| probeNames-methods | Methods for accessing the Probe Names |
| ProbeSet-class | Class ProbeSet |
| ProgressBarText-class | Class "ProgressBarText" |
| read.affybatch | Read CEL files into an AffyBatch |
| read.probematrix | Read CEL file data into PM or MM matrices |
| rma | Robust Multi-Array Average expression measure |
| SpikeIn | SpikeIn Experiment Data: ProbeSet Example |
| summary | Probe Set Summarizing Functions |
| tukey.biweight | One-step Tukey's biweight |
| whatcdf | Find which CDF corresponds |
| xy2indices | Functions to convert indices to x/y (and reverse) |