getGlobalMetrics: Global Metrics of Expression Data

Description Usage Arguments Details Value See Also

Description

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

Usage

1

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 Dec. 14, 2018, 3:05 p.m.