Man pages for affy
Methods for Affymetrix Oligonucleotide Arrays

AffyBatch-classClass AffyBatch
affy-deprecatedDeprecated functions in package 'affy'
affy-optionsOptions for the affy package
AffyRNAdegFunction to assess RNA degradation in Affymetrix GeneChip...
affy.scalevalue.exprSetScale normalization for expreSets
barplot.ProbeSetshow a ProbeSet as barplots
bg.adjustBackground adjustment (internal function)
bgcBackground Correction
cdfenv.exampleExample cdfenv
cdfFromBioCFunctions to obtain CDF files
cleancdfnameClean Affymetrix's CDF name
debug.affy123Debugging Flag
expressoFrom raw probe intensities to expression values
expressoWidgetA widget for users to pick correction methods Li and Wong Model to a Probe Set
generateExprSet-methodsgenerate a set of expression values
generateExprVal.method.avgdiffGenerate an expression value from the probes informations
generateExprVal.method.playeroutGenerate an expression value from the probes informations
generateExprVal-methodsCompute a summary expression value from the probes...
hlogHybrid Log
justrmaRead CEL files into an ExpressionSet
list.celfilesList the Cel Files in a Directory/Folder
maffy.subsetSelect Subset
MAplotRelative M vs. A plots
mas5MAS 5.0 expression measure
mas5callsMAS 5.0 Absolute Detection
merge.AffyBatchmerge two AffyBatch objects
mva.pairsM vs. A Matrix
normalize.constantScale probe intensities
normalize.contrastNormalize intensities using the contrasts method
normalize.invariantsetInvariant Set normalization
normalize.loessScale microarray data
normalize-methodsNormalize Affymetrix Probe Level Data - methods
normalize.qsplineNormalize arrays
normalize.quantilesQuantile Normalization
normalize.quantiles.robustRobust Quantile Normalization
pairs.AffyBatchplot intensities using 'pairs'
plot.densityPlot Densities
plotLocationPlot a location on a cel image
plot.ProbeSetplot a probe set
pmcorrectPM Correction
ppsetApplyApply a function over the ProbeSets in an AffyBatch
probeMatch-methodsMethods for accessing perfect matches and mismatches
probeNames-methodsMethods for accessing the Probe Names
ProbeSet-classClass ProbeSet
ProgressBarText-classClass "ProgressBarText"
read.affybatchRead CEL files into an AffyBatch
read.probematrixRead CEL file data into PM or MM matrices
rmaRobust Multi-Array Average expression measure
setAffyOptions~~function to set options ~~
SpikeInSpikeIn Experiment Data: ProbeSet Example
summaryProbe Set Summarizing Functions
tukey.biweightOne-step Tukey's biweight
whatcdfFind which CDF corresponds
xy2indicesFunctions to convert indices to x/y (and reverse)
affy documentation built on Nov. 8, 2020, 8:18 p.m.