xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Bioconductor version: Release (2.11)
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>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("xps")
To cite this package in a publication, start R and enter:
citation("xps")
Documentation
| 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 |
Details
| biocViews | DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription |
| Version | 1.18.1 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | GPL (>= 2.0) |
| Depends | R (>= 2.6.0), methods, utils |
| Imports | |
| Suggests | tools |
| System Requirements | root_v5.32.01 |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | xps_1.18.1.tar.gz |
| Windows Binary | |
| MacOS 10.5 (Leopard) | xps_1.18.1.tgz |
| Package Downloads Report | Download Stats |
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