Methods for analyzing microarray data using Local Pooled Error (LPE) method

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Documentation for package ‘LPE’ version 1.81.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
Ley	Gene Expression Data from Mouse Immune response study, (2002)
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