Package: affy 1.85.0
Robert D. Shear
affy: Methods for Affymetrix Oligonucleotide Arrays
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
Authors:
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affy.pdf |affy.html✨
affy/json (API)
NEWS
| # Install 'affy' in R: |
| install.packages('affy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rafalab/affy/issues
- SpikeIn - SpikeIn Experiment Data: ProbeSet Example
- cdfenv.example - Example cdfenv
- mapCdfName - Clean Affymetrix's CDF name
On BioConductor:affy-1.85.0(bioc 3.21)affy-1.84.0(bioc 3.20)
microarrayonechannelpreprocessing
Last updated 2 months agofrom:501ff3078e. Checks:ERROR: 2 WARNING: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 30 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.5-linux-x86_64 | ERROR | Nov 30 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 30 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 30 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 30 2024 |
Exports:.setAffyOptions$.AffyBatchaffy.scalevalue.exprSetAffyRNAdegAllButCelsForReadAffyavdiffbarplotbarplot.ProbeSetbg.adjustbg.correctbg.correct.masbg.correct.nonebg.correct.rmabg.parametersbgcorrect.methodsboxplotcdfFromBioCcdfFromEnvironmentcdfFromLibPathcdfNamecheckValidFilenamescleancdfnameclosecomputeExprSetdebug.affy123express.summary.statexpress.summary.stat.methodsexpressoexpressoWidgetexprsexprs<-featureNamesfit.li.wonggeneNamesgenerateExprSet.methodsgenerateExprVal.method.avgdiffgenerateExprVal.method.liwonggenerateExprVal.method.masgenerateExprVal.method.medianpolishgenerateExprVal.method.playeroutgetCdfInfohisthlogimageindexProbesindices2xyintensityintensity<-just.rmajustRMAli.wonglist.celfilesloess.normalizema.plotmaffy.normalizemaffy.subsetMAplotmas5mas5.detectionmas5callsmas5calls.AffyBatchmas5calls.ProbeSetMboxmedianpolishmerge.AffyBatchmmmm<-mmindexmultiloessmva.pairsnormalize.AffyBatch.constantnormalize.AffyBatch.contrastsnormalize.AffyBatch.invariantsetnormalize.AffyBatch.loessnormalize.AffyBatch.methodsnormalize.AffyBatch.qsplinenormalize.AffyBatch.quantilesnormalize.AffyBatch.quantiles.robustnormalize.constantnormalize.invariantsetnormalize.loessnormalize.methodsnormalize.qsplineopenpairs.AffyBatchplayerout.costfunctionplot.ProbeSetplotAffyRNAdegplotDensityplotDensity.AffyBatchplotLocationpmpm<-pmcorrect.maspmcorrect.methodspmcorrect.pmonlypmcorrect.subtractmmpmindexppset.ttestppsetApplyprobeNamesprobesprobesetread.affybatchread.probematrixReadAffyrmasampleNamesse.exprsshowsimplemultiLoesssummaryAffyRNAdegtukey.biweighttukeybiweightupDate.bgcorrect.methodsupDate.express.summary.stat.methodsupDate.generateExprSet.methodsupDate.normalize.AffyBatch.methodsupDate.pmcorrect.methodsupdateMeupdateObjectwhatcdfxy2indices
Dependencies:affyioBiobaseBiocGenericsBiocManagergenericspreprocessCorezlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ~~function to set options ~~ | .setAffyOptions |
| Deprecated functions in package 'affy' | loess.normalize maffy.normalize multiloess simplemultiLoess |
| Options for the affy package | affy-options |
| Scale normalization for expreSets | affy.scalevalue.exprSet |
| Class AffyBatch | $.AffyBatch AffyBatch AffyBatch,ANY AffyBatch-class bg.correct,AffyBatch,character-method boxplot,AffyBatch-method cdfName cdfName,AffyBatch-method checkValidFilenames col,AffyBatch-method computeExprSet,AffyBatch,character,character-method dim,AffyBatch-method exprs,AffyBatch-method exprs<-,AffyBatch,ANY-method featureNames,AffyBatch-method featureNames<-,AffyBatch-method geneNames geneNames,AffyBatch-method geneNames<- geneNames<-,AffyBatch,ANY-method getCdfInfo getCdfInfo,AffyBatch-method hist,AffyBatch-method image image,AffyBatch-method indexProbes indexProbes,AffyBatch,character-method indexProbes,AffyBatch,missing-method indexProbes,AffyBatch-method initialize,AffyBatch-method intensity intensity,AffyBatch-method intensity<- intensity<-,AffyBatch-method length,AffyBatch-method mm,AffyBatch-method mm<-,AffyBatch,ANY-method mmindex mmindex,AffyBatch-method pm,AffyBatch-method pm<-,AffyBatch,ANY-method pmindex pmindex,AffyBatch-method probeNames,AffyBatch-method probes probes,AffyBatch-method probeset probeset,AffyBatch-method row,AffyBatch-method se.exprs,AffyBatch-method se.exprs<-,AffyBatch-method show,AffyBatch-method updateObject,AffyBatch-method [,AffyBatch-method [<-,AffyBatch-method [[,AffyBatch-method |
| Function to assess RNA degradation in Affymetrix GeneChip data. | AffyRNAdeg plotAffyRNAdeg summaryAffyRNAdeg |
| show a ProbeSet as barplots | barplot.ProbeSet |
| Background adjustment (internal function) | bg.adjust bg.parameters |
| Background Correction | bg.correct bg.correct.mas bg.correct.none bg.correct.rma |
| Example cdfenv | cdfenv.example |
| Functions to obtain CDF files | cdfFromBioC cdfFromEnvironment cdfFromLibPath |
| Clean Affymetrix's CDF name | cleancdfname mapCdfName |
| Debugging Flag | debug.affy123 |
| From raw probe intensities to expression values | bgcorrect expresso |
| A widget for users to pick correction methods | expressoWidget |
| Fit Li and Wong Model to a Probe Set | fit.li.wong li.wong |
| generate a set of expression values | computeExprSet generateExprSet-methods generateExprSet.methods upDate.generateExprSet.methods |
| Compute a summary expression value from the probes intensities | express.summary.stat express.summary.stat-methods express.summary.stat.methods upDate.express.summary.stat.methods |
| Generate an expression value from the probes informations | generateExprVal.method.avgdiff generateExprVal.method.liwong generateExprVal.method.mas generateExprVal.method.medianpolish |
| Generate an expression value from the probes informations | generateExprVal.method.playerout playerout.costfunction |
| Hybrid Log | hlog |
| Read CEL files into an ExpressionSet | just.rma justRMA |
| List the Cel Files in a Directory/Folder | list.celfiles |
| Relative M vs. A plots | ma.plot MAplot MAplot,AffyBatch-method Mbox Mbox,AffyBatch-method |
| MAS 5.0 expression measure | mas5 |
| MAS 5.0 Absolute Detection | mas5.detection mas5calls mas5calls,AffyBatch-method mas5calls,ProbeSet-method mas5calls.AffyBatch mas5calls.ProbeSet |
| merge two AffyBatch objects | merge.AffyBatch |
| M vs. A Matrix | mva.pairs |
| Normalize Affymetrix Probe Level Data - methods | bgcorrect.methods normalize,AffyBatch-method normalize.AffyBatch normalize.AffyBatch.methods normalize.methods normalize.methods,AffyBatch-method pmcorrect.methods upDate.bgcorrect.methods upDate.normalize.AffyBatch.methods upDate.pmcorrect.methods |
| Scale probe intensities | normalize.AffyBatch.constant normalize.constant |
| Normalize intensities using the contrasts method | normalize.AffyBatch.contrasts normalize.contrasts |
| Invariant Set normalization | normalize.AffyBatch.invariantset normalize.invariantset |
| Scale microarray data | normalize.AffyBatch.loess normalize.loess |
| Normalize arrays | normalize.AffyBatch.qspline normalize.qspline qspline-normalize |
| Quantile Normalization | normalize.AffyBatch.quantiles |
| Robust Quantile Normalization | normalize.AffyBatch.quantiles.robust |
| plot intensities using 'pairs' | pairs.AffyBatch |
| plot a probe set | plot.ProbeSet |
| Plot Densities | plotDensity plotDensity.AffyBatch |
| Plot a location on a cel image | plotLocation |
| PM Correction | pmcorrect pmcorrect.mas pmcorrect.pmonly pmcorrect.subtractmm |
| Apply a function over the ProbeSets in an AffyBatch | ppset.ttest ppsetApply |
| Methods for accessing perfect matches and mismatches | mm mm<- pm pm<- probeMatch probeMatch-methods |
| Methods for accessing the Probe Names | probeNames probeNames-methods probeNames<- |
| Class ProbeSet | barplot,ProbeSet-method colnames,ProbeSet-method express.summary.stat,ProbeSet,character,character-method mm,ProbeSet-method mm<-,ProbeSet,matrix-method pm,ProbeSet-method pm<-,ProbeSet,matrix-method ProbeSet-class sampleNames,ProbeSet-method show,ProbeSet-method |
| Class "ProgressBarText" | close,ProgressBarText-method initialize,ProgressBarText-method open,ProgressBarText-method ProgressBarText-class updateMe updateMe,ProgressBarText-method |
| Read CEL files into an AffyBatch | AllButCelsForReadAffy read.affybatch ReadAffy |
| Read CEL file data into PM or MM matrices | read.probematrix |
| Robust Multi-Array Average expression measure | rma |
| SpikeIn Experiment Data: ProbeSet Example | concentrations SpikeIn |
| Probe Set Summarizing Functions | avdiff medianpolish summary tukeybiweight |
| One-step Tukey's biweight | tukey.biweight |
| Find which CDF corresponds | whatcdf |
| Functions to convert indices to x/y (and reverse) | indices2xy xy2indices |
