Ley                     Gene Expression Data from Mouse Immune response
                        study, (2002)
am.trans                Transform replicated arrays into (A,M) format
baseOlig.error          Evaluates LPE variance function of M for
                        quantiles of A within and experimental
                        condition and then interpolates it for all
                        genes.
baseOlig.error.step1    Evaluates LPE variance function of M for
                        quantiles of A within and experimental
                        condition by divinding the A in 100 intervals.
baseOlig.error.step2    Evaluates LPE variance function of M for
                        quantiles of A within and experimental
                        condition. It is based on the adaptive number
                        of intervals.
fdr.adjust              FDR adjustment procedures
fixbounds.predict.smooth.spline
                        Makes the predicted variance non negative
iqr                     Inter-quartile range
lowess.normalize        lowess normalization of the data (based on M vs
                        A graph)
lpe                     Evaluates local pooled error significance test
mt.rawp2adjp.LPE        Adjusted p-values for simple multiple testing
                        procedures
n.genes.adaptive.int    Calcuates the number of genes in various
                        intervals adaptively.
permute                 Calculating all possible permutations of a
                        vector
preprocess              Preprocessing the data (IQR normalization,
                        thresholding, log- transformation, and lowess
                        normalization)
quan.norm               Finding quartile range
quartile.normalize      Normalization based on quartile range
resamp.adj              Resampling based fdr adjustment