unitestFilter-methods

unitestFilter

unitestFilter<-

object

character vector <code>c(cutoff, variable)</code>.

value

This method initializes the Unitest Filter. 
 Applying an unitest such as the <code>t.test</code> to two groups returns the p-value for the test
 and the value of the t-statistic. The Unitest Filter allows to select only rows satisfying
 e.g. a certain p-value as cutoff. 
 The Unitest Filter flags all rows with: <code>flag = (variable <= cutoff)<="" code="">Usage<code>unitestFilter(object)</code> 
<code>unitestFilter(object, value)&lt;-</code>
</=></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

unitestFilter-methods function

This method initializes the Unitest Filter. 
 Applying an unitest such as the <code>t.test</code> to two groups returns the p-value for the test
 and the value of the t-statistic. The Unitest Filter allows to select only rows satisfying
 e.g. a certain p-value as cutoff. 
 The Unitest Filter flags all rows with: <code>flag = (variable <= cutoff)</code>

Usage

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

	`cutoff`:
the cutoff level for the filter.
`variable`:	`variable="pval"` (default): p-value.

`variable="stat"`: univariate statistic.
	`variable="padj"`: optional adjusted p-value.

unitestFilter-methods: Unitest Filter

Description

Arguments

Value

Details

Examples