Calculate parameters for differential expression test base on absolute counts differences

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Description

Calculate parameters for each gene (the moderating basemean and dispersions)

Usage

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callParameter(object, replaceOutliers = TRUE, ...)

Arguments

object

a ABSDataSet object.

replaceOutliers

switch for outlier replacement, default is TRUE.

...

parameters past to ReplaceOutliersByMAD

Details

shifted and calculate a set of parameters from normalized counts table before callDEs

Value

A ABSDataSet object with absolute differences, basemean, mean of each group, variance, log2 of foldchange, named as 'absD', 'baseMean', 'Amean', 'Bmean', 'Variance' and 'foldChange', respectively. Use the results to get access it and plotDifftoBase to plot it.

Note

This function should run after normalFactors or providing size factors.

Examples

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data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- callParameter(obj)
head(results(obj,c("foldChange","absD","baseMean")))
plotDifftoBase(obj)

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