To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("xps")

In most cases, you don't need to download the package archive at all.

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 (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("xps")

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 1.38.0
In Bioconductor since BioC 2.2 (R-2.7) (9.5 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
Build Report  

Package Archives

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

Source Package xps_1.38.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) xps_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/xps
Package Short Url http://bioconductor.org/packages/xps/
Package Downloads Report Download Stats

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