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
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Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Bioconductor version: Release (3.5)
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")
| R Script | 1. XPS Vignette: Overview | |
| R Script | 2. XPS Vignette: Classes | |
| R Script | 3. XPS Vignette: Comparison APT vs XPS | |
| R Script | 4. XPS Vignette: Function express() | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS | |
| Text | INSTALL |
Details
| biocViews | DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription |
| Version | 1.36.1 |
| 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 |
| 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_1.36.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | xps_1.36.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/xps |
| Package Short Url | http://bioconductor.org/packages/xps/ |
| Package Downloads Report | Download Stats |
Documentation »
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