ABSSeq (version 1.8.0)

callParameterwithoutReplicates: Calculate parameters for differential expression test base on absolute counts differences without replicates

Description

Calculate parameters for each gene (the moderating basemean and dispersions), without replicates

Usage

callParameterwithoutReplicates(object)

Arguments

object

a ABSDataSet object.

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

Details

buliding a pseudo group to esitimate parameter by mean difference. shifted and calculate a set of parameters from normalized counts table before callDEs

Examples

data(simuN5)
obj <- ABSDataSet(counts=(simuN5$counts)[,c(1,2)], groups=factor(c(1,2)))
obj <- normalFactors(obj)
obj <- callParameterwithoutReplicates(obj)
obj <- callDEs(obj)
head(results(obj))