varFilter-methods: Variance Filter

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

This method initializes the Variance Filter.
The Variance Filter flags all rows with: flag = (var/mean >= cutoff)

Usage

varFilter(object)
varFilter(object, value)<-

Arguments

object	object of class PreFilter.
value	numeric vector c(cutoff, trim, epsilon).

Details

The method varFilter initializes the following parameters:

	cutoff:	the cutoff level for the filter.
	trim:	the trim value for trimmed mean (default is trim=0).
	epsilon:	value to replace mean (default is epsilon=0.01):
		epsilon > 0: replace mean=0 with epsilon.
		epsilon = 0: always set mean=1.

Note, that for epsilon = 0 the filter flags all rows with: variance >= cutoff

Value

An initialized PreFilter object.

Author(s)

Christian Stratowa

Examples

prefltr <- PreFilter()
varFilter(prefltr) <- c(0.6,0.02,0.01)
str(prefltr)

xps documentation built on Nov. 8, 2020, 6 p.m.