To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("xps")
In most cases, you don't need to download the package archive at all.
xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Bioconductor version: 2.14
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:
source("http://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 |
Details
| biocViews | DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription |
| Version | 1.24.1 |
| 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_v5.34.05 |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | xps_1.24.1.tar.gz |
| Windows Binary | xps_1.24.1.zip (32-bit only) |
| Mac OS X 10.6 (Snow Leopard) | xps_1.24.1.tgz |
| Mac OS X 10.9 (Mavericks) | xps_1.24.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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