MAplot-methods          MA plots
basecontent             Sequence Base Contents
basicRMA                Simplified Interface to RMA
boxplot-methods         Boxplot
chromosome              Accessor for chromosome information
crlmm                   Genotype Calls
darkColors              Create set of colors, interpolating through a
                        set of preferred colors.
getAffinitySplineCoefficients
                        Estimate affinity coefficients.
getBaseProfile          Compute and plot nucleotide profile.
getContainer            Get container information for NimbleGen Tiling
                        Arrays.
getCrlmmSummaries       Function to get CRLMM summaries saved to disk
getNgsColorsInfo        Helper function to extract color information
                        for filenames on NimbleGen arrays.
getPlatformDesign       Retrieve Platform Design object
getX                    Accessors for physical array coordinates.
hist-methods            Density estimate
image-methods           Display a pseudo-image of a microarray chip
justSNPRMA              Summarization of SNP data
list.xysfiles           List XYS files
mm                      Accessors and replacement methods for the
                        PM/MM/BG matrices.
mmSequence              Probe Sequeces
mmindex                 Accessors for PM, MM or background probes
                        indices.
oligo-package           The oligo package: a tool for low-level
                        analysis of oligonucleotide arrays
plotM-methods           Methods for Log-Ratio plotting
pmAllele                Access the allele information for PM probes.
pmFragmentLength        Access the fragment length for PM probes.
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-methods             RMA - Robust Multichip Average algorithm
sequenceDesignMatrix    Create design matrix for sequences
snprma                  Preprocessing SNP Arrays
summarize               Tools for microarray preprocessing
