quantileFilter-methods

quantileFilter

quantileFilter<-

object

numeric vector <code>c(cutoff, loquantile, hiquantile)</code>.

value

This method initializes the Quantile Filter. 
 The Quantile Filter flags all rows with: <code>flag = (quantile[high]/quantile[low] >= cutoff)</code>Usage<code>quantileFilter(object)</code> 
<code>quantileFilter(object, value)&lt;-</code>

methods

The package handles pre-processing, normalization, filtering
and analysis of Affymetrix GeneChip expression arrays, including exon
arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST)
and plate arrays on computers with 1 GB RAM only. It imports Affymetrix
.CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA,
MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to
XPS (eXpression Profiling System), which is based on ROOT, an object-oriented
framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite
for the usage of this package, however, no knowledge of ROOT is required.
ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

Christian Stratowa

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

quantileFilter-methods function

This method initializes the Quantile Filter. 
 The Quantile Filter flags all rows with: <code>flag = (quantile[high]/quantile[low] >= cutoff)</code>

Usage

<code>quantileFilter(object)</code> 
<code>quantileFilter(object, value)<-</code>

	`cutoff`:
the cutoff level for the filter.
`loquantile`:	value for low quantile (default is `loquantile=0.05`).

quantileFilter-methods: Quantile Filter

Description

Arguments

Value

Details

Examples