DBPDInfo-class          Class "DBPDInfo"
ExonFeatureSet-class    "FeatureSet" Extensions
FeatureSet-class        Classes for Feature level data
MAplot-methods          MA plots
PDInfo-class            Classes "PDInfo" and "SNPPDInfo"
SnpCallSet-class        "SnpSet" Extensions
SnpQSet-class           Class "SnpQSet"
antisenseThetaA         Summarized Measures for SNP
basecontent             Sequence Base Contents
boxplot                 Boxplot
crlmm                   Genotype Calls
featureIndex            Indexes for features in the expression matrix
featureNames-methods    Retrieve featureNames
genomeBuild             Genome Build Information
getA                    Compute average log-intensities / log-ratios
getChrXIndex            Internals
getCrlmmSummaries       Function to get CRLMM summaries saved to disk
getPlatformDesign       Retrieve Platform Design object
hist                    Density estimate
image                   Display a Color Image
justSNPRMA              Summarization of SNP data
kind                    Array type
list.celfiles           List CEL/XYS files
listFeatureFields       List fields in the (pm/mm)feature table
manufacturer            Accessor to the manufacturer slot.
mm                      Accessor to the PM/MM matrices
mmSequence              Probe Sequeces
mmindex                 Extract PM or MM indexes
nProbes                 Count number of probes
ncol                    ~~function to do ... ~~
oligo-package           The oligo package: a tool for analysis of
                        oligonucleotide arrays
platform                Retrieve/replace platform information
platformDesign-class    Class "platformDesign"
plotM-methods           Methods for Log-Ratio plotting
pmAllele                Access the allele information for PM probes.
pmChr                   Accessor for chromosome information
pmPosition              Accessor to position information
pmStrand                Accessor to the strand information
probeNames              Accessor to feature names
read.celfiles           Parser to CEL files
read.xysfiles           Parser to XYS files
readSummaries           Read summaries generated by crlmm
rma                     RMA
sequenceDesignMatrix    Create design matrix for sequences
snprma                  Preprocessing SNP Arrays
