getGlobalMetrics: Global Metrics of Expression Data

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Global Metrics of Expression Data

Description

Get various statistical measurement metrics about a matrix of expression data, typically of microarray oligo/gene intensities

Usage

getGlobalMetrics(m)

Arguments

m	a numeric matrix of expression values, with a row for each gene/oligo and a column for each sample

Details

This function measures several metrics about the data, all of which may be useful for the various types of data normalization common to microarrays.

Value

A list of numeric scalars. For each scalar, the mean of that metric measured separately for each sample, is the value reported.

mean	the average mean of each column of m
median	the average median of each column of m
floor	the average floor of each column of m
max	the average max of each column of m
min	the average min of each column of m
logmean	the average logmean (geometric mean) of each column of m. See logmean
baseline	the average baseline of each column of m. This is measured using intergenic and negative control probes when available, and by DKM if not.
DKM	the average DKM (Density Kernel Mode) of each column of m. See getDensityKernelMode

See Also

duffyRMA

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