DKMshift: Density Kernel Mode Linear Shift

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Density Kernel Mode Linear Shift

Description

Low level routine to apply the DKM background correction step of RMA

Usage

DKMshift(m, target = getGlobalMetrics(obj)$DKM)

Arguments

m	numeric matrix of expression data, with a row for each gene/oligo, and a column for each sample
target	target value for the mode of the density kernel for each column

Details

This function implements the background subtraction step of RMA. It prevents the creation of negative expression values, by a linear compaction of values smaller than target.

Value

a numeric matrix of the same size as m, with the background correction linear shift applied to all columns

See Also

duffyRMA, for details about the RMA implementation. getDensityKernelMode, for calculating DKM. getGlobalMetrics, for various metrics of an expression matrix including the mean DKM value.

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.