addXYfromGAL            Computing the coordinates of the spots on a
                        slide
aqm.boxplot             Compute boxplots, density plots, heatmap, PCA
                        biplot on a aqmobj.prepdata object.
aqm.maplot              Performs MA-plots on aqmobj.prepdata objects.
aqm.meansd              Performs Mean/SD plot on aqmobj.prepdata
                        objects.
aqm.plot                Performs plots from aqm objects.
aqm.pmmm                Performs perfect match versus mismatch density
                        plots.
aqm.prepaffy            Preparation of Affymetrix experiments for RLE
                        and NUSE.
aqm.prepdata            Generate an object aqmobj.prepdata to be called
                        by the aqm functions.
aqm.probesmap           Performs probes mapping on aqmobj.prepdata
                        objects.
aqm.qcstats             Performs QCstats plot on AffyBatch.
aqm.rle                 Performs RLE and NUSE plots on aqmobj.prepaffy
                        objects.
aqm.rnadeg              Computes RNA degradation plot on AffyBatch.
aqm.spatial             Performs spatial distribution representation of
                        the arrays from aqmobj.prepdata objects.
aqm.spatialbg           Performs spatial distribution representation of
                        background intensities of the arrays from
                        aqmobj.prepdata objects.
aqm.writereport         Writes a report from objects produced with
                        aqm.xxx functions.
aqmobj.box-class        Class to contain data generated from the
                        aqm.boxplot, aqm.heatmap, aqm.maplot,
                        aqm.spatial, aqm.nuse and aqm.rle functions.
aqmobj.dens-class       Class to contain data generated from
                        aqm.density, aqm.pca, aqm.spatialbg,
                        aqm.probesmap, aqm.qcs.
aqmobj.msd-class        Class to contain data generated from
                        aqm.meansd.
aqmobj.pmmm-class       Class to contain data generated from aqm.pmmm.
aqmobj.prepaffy-class   Class to contain data generated from
                        aqm.prepaffy.
aqmobj.prepdata-class   Class to contain data generated from
                        aqm.prepdata.
aqmobj.rnadeg-class     Class to contain data generated from
                        aqm.rnadegplot.
arrayQualityMetrics     Quality metrics for microarray experiments
ksOutliers              Function for outlier determing potential
                        outliers
