xps

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see xps.

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

Bioconductor version: 3.12

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.

Author: Christian Stratowa, Vienna, Austria

Maintainer: Christian Stratowa <cstrato at aon.at>

Citation (from within R, enter citation("xps")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("xps")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("xps")

1. XPS Vignette: Overview	PDF	R Script
2. XPS Vignette: Classes	PDF	R Script
3. XPS Vignette: Comparison APT vs XPS	PDF	R Script
4. XPS Vignette: Function express()	PDF	R Script
Reference Manual	PDF
README	Text
NEWS	Text
INSTALL	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription
Version	1.50.0
In Bioconductor since	BioC 2.2 (R-2.7) (16 years)
License	GPL (>= 2.0)
Depends	R (>= 2.6.0), methods, utils
Imports
System Requirements	GNU make, root_v5.34.36 - See README file for installation instructions.
URL

Suggests	tools
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	xps_1.50.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/xps
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/xps
Package Short Url	https://bioconductor.org/packages/xps/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.12	Source Archive