xps

DOI: 10.18129/B9.bioc.xps    

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

Bioconductor version: Release (3.11)

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>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	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		Reference Manual
Text		README
Text		NEWS
Text		INSTALL

Details

biocViews	DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription
Version	1.48.0
In Bioconductor since	BioC 2.2 (R-2.7) (12.5 years)
License	GPL (>= 2.0)
Depends	R (>= 2.6.0), methods, utils
Imports
LinkingTo
Suggests	tools
SystemRequirements	GNU make, root_v5.34.36 - See README file for installation instructions.
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	xps_1.48.0.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 3.11	Source Archive