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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
| $.AffyBatch | Class AffyBatch |
| .setAffyOptions | ~~function to set options ~~ |
| 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 |
| affybatch.example | AffyBatch instance affybatch.example |
| affybatch.example2 | AffyBatch instance affybatch.example |
| AffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
| AllButCelsForReadAffy | Read CEL files into an AffyBatch |
| avdiff | Probe Set Summarizing Functions |
| barplot,ProbeSet-method | Class ProbeSet |
| barplot.ProbeSet | show a ProbeSet as barplots |
| bg.adjust | Background ajustment (internal function) |
| bg.correct | Background Correction |
| bg.correct,AffyBatch,character-method | Class AffyBatch |
| bg.correct.mas | Background Correction |
| bg.correct.none | Background Correction |
| bg.correct.rma | Background Correction |
| bg.correct.rma2 | Background Correction |
| bg.parameters | Background ajustment (internal function) |
| bgcorrect | From raw probe intensities to expression values |
| boxplot,AffyBatch-method | Class AffyBatch |
| cdfenv.example | Example cdfenv |
| cdfFromBioC | Functions to obtain CDF files |
| cdfFromData | Functions to obtain CDF files |
| cdfFromEnvironment | Functions to obtain CDF files |
| cdfFromLibPath | Functions to obtain CDF files |
| cdfName | Class AffyBatch |
| cdfName,AffyBatch-method | Class AffyBatch |
| checkValidFilenames | Class AffyBatch |
| cleancdfname | Clean Affymetrix's CDF name |
| close,ProgressBarText-method | Class "ProgressBarText" |
| col,AffyBatch-method | Class AffyBatch |
| colnames,ProbeSet-method | Class ProbeSet |
| computeExprSet | generate a set of expression values |
| computeExprSet,AffyBatch,character,character-method | Class AffyBatch |
| concentrations | SpikeIn Experiment Data: ProbeSet Example |
| debug.affy123 | Debugging Flag |
| dim,AffyBatch-method | Class AffyBatch |
| express.summary.stat | Compute a summary expression value from the probes intensities |
| express.summary.stat,ProbeSet,character,character-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,AffyBatch-method | Class AffyBatch |
| exprs<-,AffyBatch,ANY-method | Class AffyBatch |
| featureNames,AffyBatch-method | Class AffyBatch |
| featureNames<-,AffyBatch-method | Class AffyBatch |
| fit.li.wong | Fit Li and Wong Model to a Probe Set |
| geneNames | Class AffyBatch |
| geneNames,AffyBatch-method | Class AffyBatch |
| geneNames<-,AffyBatch,ANY-method | Class AffyBatch |
| generateExprSet-methods | generate a set of expression values |
| generateExprSet.methods | generate a set of expression values |
| generateExprVal | Compute a summary expression value from the probes intensities |
| generateExprVal-methods | Compute a summary expression value from the probes intensities |
| 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 |
| generateExprVal.methods | Compute a summary expression value from the probes intensities |
| getCdfInfo | Class AffyBatch |
| getCdfInfo,AffyBatch-method | Class AffyBatch |
| hist,AffyBatch-method | Class AffyBatch |
| hlog | Hybrid Log |
| image | Class AffyBatch |
| image,AffyBatch-method | Class AffyBatch |
| indexProbes | Class AffyBatch |
| indexProbes,AffyBatch,character-method | Class AffyBatch |
| indexProbes,AffyBatch,missing-method | Class AffyBatch |
| indexProbes,AffyBatch-method | Class AffyBatch |
| indices2xy | Functions to convert indices to x/y (and reverse) |
| initialize,AffyBatch-method | Class AffyBatch |
| initialize,ProgressBarText-method | Class "ProgressBarText" |
| intensity | Class AffyBatch |
| intensity,AffyBatch-method | Class AffyBatch |
| intensity<-,AffyBatch-method | Class AffyBatch |
| just.rma | Read CEL files into an ExpressionSet |
| justRMA | Read CEL files into an ExpressionSet |
| length,AffyBatch-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 | Normalize arrays |
| ma.plot | Relative M vs. A plots |
| mapCdfName | Clean Affymetrix's CDF name |
| MAplot | Relative M vs. A plots |
| MAplot,AffyBatch-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,AffyBatch-method | MAS 5.0 Absolute Detection |
| mas5calls,ProbeSet-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,AffyBatch-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,AffyBatch-method | Class AffyBatch |
| mm,ProbeSet-method | Class ProbeSet |
| mm<-,AffyBatch,ANY-method | Class AffyBatch |
| mm<-,ProbeSet,matrix-method | Class ProbeSet |
| mmindex | Class AffyBatch |
| mmindex,AffyBatch-method | Class AffyBatch |
| mva.pairs | M vs. A Matrix |
| normalize | Normalize - generic |
| normalize,AffyBatch-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 | Invariante 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 | Invariante Set normalization |
| normalize.loess | Scale microarray data |
| normalize.methods | Normalize Affymetrix Probe Level Data - methods |
| normalize.methods,AffyBatch-method | Normalize Affymetrix Probe Level Data - methods |
| normalize.qspline | Normalize arrays |
| open,ProgressBarText-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 |
| plotLocation | Plot a location on a cel image |
| pm | Methods for accessing perfect matches and mismatches |
| pm,AffyBatch-method | Class AffyBatch |
| pm,ProbeSet-method | Class ProbeSet |
| pm<-,AffyBatch,ANY-method | Class AffyBatch |
| pm<-,ProbeSet,matrix-method | Class ProbeSet |
| pmcorrect | PM Correction |
| pmindex | Class AffyBatch |
| pmindex,AffyBatch-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,AffyBatch-method | Class AffyBatch |
| probeNames-methods | Methods for accessing the Probe Names |
| probes | Class AffyBatch |
| probes,AffyBatch-method | Class AffyBatch |
| probeset | Class AffyBatch |
| probeset,AffyBatch-method | Class AffyBatch |
| ProbeSet-class | Class ProbeSet |
| 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,AffyBatch-method | Class AffyBatch |
| sampleNames,ProbeSet-method | Class ProbeSet |
| se.exprs,AffyBatch-method | Class AffyBatch |
| se.exprs<-,AffyBatch-method | Class AffyBatch |
| show,AffyBatch-method | Class AffyBatch |
| show,ProbeSet-method | Class ProbeSet |
| 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,ProgressBarText-method | Class "ProgressBarText" |
| updateObject,AffyBatch-method | Class AffyBatch |
| whatcdf | Find which CDF corresponds |
| xy2indices | Functions to convert indices to x/y (and reverse) |
| [,AffyBatch-method | Class AffyBatch |
| [<-,AffyBatch-method | Class AffyBatch |
| [[,AffyBatch-method | Class AffyBatch |