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A B C D E F G H I J L M N O P Q R S T U W X misc
| affy-options | Options for the affy package |
| affy.scalevalue.exprSet | Scale normalization for expreSets |
| AffyBatch | Class AffyBatch |
| AffyBatch,ANY | Class AffyBatch |
| AffyBatch-class | Class AffyBatch |
| AffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
| AllButCelsForReadAffy | Read CEL files into an AffyBatch |
| avdiff | Probe Set Summarizing Functions |
| barplot-method | Class ProbeSet |
| barplot.ProbeSet | show a ProbeSet as barplots |
| bg.adjust | Background adjustment (internal function) |
| bg.correct | Background Correction |
| bg.correct-method | Class AffyBatch |
| bg.correct.mas | Background Correction |
| bg.correct.none | Background Correction |
| bg.correct.rma | Background Correction |
| bg.parameters | Background adjustment (internal function) |
| bgcorrect | From raw probe intensities to expression values |
| bgcorrect.methods | Normalize Affymetrix Probe Level Data - methods |
| boxplot-method | Class AffyBatch |
| cdfenv.example | Example cdfenv |
| cdfFromBioC | Functions to obtain CDF files |
| cdfFromEnvironment | Functions to obtain CDF files |
| cdfFromLibPath | Functions to obtain CDF files |
| cdfName | Class AffyBatch |
| cdfName-method | Class AffyBatch |
| checkValidFilenames | Class AffyBatch |
| cleancdfname | Clean Affymetrix's CDF name |
| close-method | Class "ProgressBarText" |
| col-method | Class AffyBatch |
| colnames-method | Class ProbeSet |
| computeExprSet | generate a set of expression values |
| computeExprSet-method | Class AffyBatch |
| concentrations | SpikeIn Experiment Data: ProbeSet Example |
| debug.affy123 | Debugging Flag |
| dim-method | Class AffyBatch |
| express.summary.stat | Compute a summary expression value from the probes intensities |
| express.summary.stat-method | Class ProbeSet |
| express.summary.stat-methods | Compute a summary expression value from the probes intensities |
| express.summary.stat.methods | Compute a summary expression value from the probes intensities |
| expresso | From raw probe intensities to expression values |
| expressoWidget | A widget for users to pick correction methods |
| exprs-method | Class AffyBatch |
| exprs<--method | Class AffyBatch |
| featureNames-method | Class AffyBatch |
| featureNames<--method | Class AffyBatch |
| fit.li.wong | Fit Li and Wong Model to a Probe Set |
| geneNames | Class AffyBatch |
| geneNames-method | Class AffyBatch |
| geneNames<- | Class AffyBatch |
| geneNames<--method | Class AffyBatch |
| generateExprSet-methods | generate a set of expression values |
| generateExprSet.methods | generate a set of expression values |
| generateExprVal.method.avgdiff | Generate an expression value from the probes informations |
| generateExprVal.method.liwong | Generate an expression value from the probes informations |
| generateExprVal.method.mas | Generate an expression value from the probes informations |
| generateExprVal.method.medianpolish | Generate an expression value from the probes informations |
| generateExprVal.method.playerout | Generate an expression value from the probes informations |
| getCdfInfo | Class AffyBatch |
| getCdfInfo-method | Class AffyBatch |
| hist-method | Class AffyBatch |
| hlog | Hybrid Log |
| image | Class AffyBatch |
| image-method | Class AffyBatch |
| indexProbes | Class AffyBatch |
| indexProbes-method | Class AffyBatch |
| indices2xy | Functions to convert indices to x/y (and reverse) |
| initialize-method | Class AffyBatch |
| initialize-method | Class "ProgressBarText" |
| intensity | Class AffyBatch |
| intensity-method | Class AffyBatch |
| intensity<- | Class AffyBatch |
| intensity<--method | Class AffyBatch |
| just.rma | Read CEL files into an ExpressionSet |
| justRMA | Read CEL files into an ExpressionSet |
| length-method | Class AffyBatch |
| li.wong | Fit Li and Wong Model to a Probe Set |
| list.celfiles | List the Cel Files in a Directory/Folder |
| loess.normalize | Deprecated functions in package 'affy' |
| ma.plot | Relative M vs. A plots |
| maffy.normalize | Deprecated functions in package 'affy' |
| mapCdfName | Clean Affymetrix's CDF name |
| MAplot | Relative M vs. A plots |
| MAplot-method | Relative M vs. A plots |
| mas5 | MAS 5.0 expression measure |
| mas5.detection | MAS 5.0 Absolute Detection |
| mas5calls | MAS 5.0 Absolute Detection |
| mas5calls-method | MAS 5.0 Absolute Detection |
| mas5calls.AffyBatch | MAS 5.0 Absolute Detection |
| mas5calls.ProbeSet | MAS 5.0 Absolute Detection |
| Mbox | Relative M vs. A plots |
| Mbox-method | Relative M vs. A plots |
| medianpolish | Probe Set Summarizing Functions |
| merge.AffyBatch | merge two AffyBatch objects |
| mm | Methods for accessing perfect matches and mismatches |
| mm-method | Class AffyBatch |
| mm-method | Class ProbeSet |
| mm<- | Methods for accessing perfect matches and mismatches |
| mm<--method | Class AffyBatch |
| mm<--method | Class ProbeSet |
| mmindex | Class AffyBatch |
| mmindex-method | Class AffyBatch |
| multiloess | Deprecated functions in package 'affy' |
| mva.pairs | M vs. A Matrix |
| normalize-method | Normalize Affymetrix Probe Level Data - methods |
| normalize.AffyBatch | Normalize Affymetrix Probe Level Data - methods |
| normalize.AffyBatch.constant | Scale probe intensities |
| normalize.AffyBatch.contrasts | Normalize intensities using the contrasts method |
| normalize.AffyBatch.invariantset | Invariant Set normalization |
| normalize.AffyBatch.loess | Scale microarray data |
| normalize.AffyBatch.methods | Normalize Affymetrix Probe Level Data - methods |
| normalize.AffyBatch.qspline | Normalize arrays |
| normalize.AffyBatch.quantiles | Quantile Normalization |
| normalize.AffyBatch.quantiles.robust | Robust Quantile Normalization |
| normalize.constant | Scale probe intensities |
| normalize.contrasts | Normalize intensities using the contrasts method |
| normalize.invariantset | Invariant Set normalization |
| normalize.loess | Scale microarray data |
| normalize.methods | Normalize Affymetrix Probe Level Data - methods |
| normalize.methods-method | Normalize Affymetrix Probe Level Data - methods |
| normalize.qspline | Normalize arrays |
| open-method | Class "ProgressBarText" |
| pairs.AffyBatch | plot intensities using 'pairs' |
| playerout.costfunction | Generate an expression value from the probes informations |
| plot.ProbeSet | plot a probe set |
| plotAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
| plotDensity | Plot Densities |
| plotDensity.AffyBatch | Plot Densities |
| plotLocation | Plot a location on a cel image |
| pm | Methods for accessing perfect matches and mismatches |
| pm-method | Class AffyBatch |
| pm-method | Class ProbeSet |
| pm<- | Methods for accessing perfect matches and mismatches |
| pm<--method | Class AffyBatch |
| pm<--method | Class ProbeSet |
| pmcorrect | PM Correction |
| pmcorrect.mas | PM Correction |
| pmcorrect.methods | Normalize Affymetrix Probe Level Data - methods |
| pmcorrect.pmonly | PM Correction |
| pmcorrect.subtractmm | PM Correction |
| pmindex | Class AffyBatch |
| pmindex-method | Class AffyBatch |
| ppset.ttest | Apply a function over the ProbeSets in an AffyBatch |
| ppsetApply | Apply a function over the ProbeSets in an AffyBatch |
| probeMatch | Methods for accessing perfect matches and mismatches |
| probeMatch-methods | Methods for accessing perfect matches and mismatches |
| probeNames | Methods for accessing the Probe Names |
| probeNames-method | Class AffyBatch |
| probeNames-methods | Methods for accessing the Probe Names |
| probeNames<- | Methods for accessing the Probe Names |
| probes | Class AffyBatch |
| probes-method | Class AffyBatch |
| probeset | Class AffyBatch |
| ProbeSet-class | Class ProbeSet |
| probeset-method | Class AffyBatch |
| ProgressBarText-class | Class "ProgressBarText" |
| qspline-normalize | Normalize arrays |
| read.affybatch | Read CEL files into an AffyBatch |
| read.probematrix | Read CEL file data into PM or MM matrices |
| ReadAffy | Read CEL files into an AffyBatch |
| rma | Robust Multi-Array Average expression measure |
| row-method | Class AffyBatch |
| sampleNames-method | Class ProbeSet |
| se.exprs-method | Class AffyBatch |
| se.exprs<--method | Class AffyBatch |
| show-method | Class AffyBatch |
| show-method | Class ProbeSet |
| simplemultiLoess | Deprecated functions in package 'affy' |
| SpikeIn | SpikeIn Experiment Data: ProbeSet Example |
| summary | Probe Set Summarizing Functions |
| summaryAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
| tukey.biweight | One-step Tukey's biweight |
| tukeybiweight | Probe Set Summarizing Functions |
| upDate.bgcorrect.methods | Normalize Affymetrix Probe Level Data - methods |
| upDate.express.summary.stat.methods | Compute a summary expression value from the probes intensities |
| upDate.generateExprSet.methods | generate a set of expression values |
| upDate.normalize.AffyBatch.methods | Normalize Affymetrix Probe Level Data - methods |
| upDate.pmcorrect.methods | Normalize Affymetrix Probe Level Data - methods |
| updateMe | Class "ProgressBarText" |
| updateMe-method | Class "ProgressBarText" |
| updateObject-method | Class AffyBatch |
| whatcdf | Find which CDF corresponds |
| xy2indices | Functions to convert indices to x/y (and reverse) |
| $.AffyBatch | Class AffyBatch |
| .setAffyOptions | ~~function to set options ~~ |
| [-method | Class AffyBatch |
| [<--method | Class AffyBatch |
| [[-method | Class AffyBatch |