diffFilter-methods: Difference Filter

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

Description

This method initializes the Difference Filter.
The difference is the maximum value minus minimum value for each row of the expression dataframe divided by the mean value of each row.
The Difference Filter flags all rows with: flag = ((max - min)/mean >= cutoff)

Usage

diffFilter(object)
diffFilter(object, value)<-

Arguments

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

Details

The method diffFilter 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: (max - min) >= cutoff

Value

An initialized PreFilter object.

Author(s)

Christian Stratowa

Examples

prefltr <- PreFilter()
diffFilter(prefltr) <- c(2.2,0.0,0.01)
str(prefltr)

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