.setAffyOptions         ~~function to set options ~~
AffyBatch-class         Class AffyBatch
AffyRNAdeg              Function to assess RNA degradation in
                        Affymetrix GeneChip data.
MAplot                  Relative M vs. A plots
ProbeSet-class          Class ProbeSet
ProgressBarText-class   Class "ProgressBarText"
SpikeIn                 SpikeIn Experiment Data: ProbeSet Example
affy-options            Options for the affy package
affy.scalevalue.exprSet
                        Scale normalization for expreSets
barplot.ProbeSet        show a ProbeSet as barplots
bg.adjust               Background adjustment (internal function)
bg.correct              Background Correction
cdfFromBioC             Functions to obtain CDF files
cdfenv.example          Example cdfenv
cleancdfname            Clean Affymetrix's CDF name
debug.affy123           Debugging Flag
express.summary.stat    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
fit.li.wong             Fit Li and Wong Model to a Probe Set
generateExprSet-methods
                        generate a set of expression values
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 ExpressionSet
list.celfiles           List the Cel Files in a Directory/Folder
loess.normalize         Deprecated functions in package 'affy'
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.AffyBatch     Normalize Affymetrix Probe Level Data - methods
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.qspline       Normalize arrays
pairs.AffyBatch         plot intensities using 'pairs'
plot.ProbeSet           plot a probe set
plotDensity             Plot Densities
plotLocation            Plot a location on a cel image
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
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
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)
