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


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Documentation for package `LPE' version 1.1.5

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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 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