Bioconductor-mirror/xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.

Getting started

Package details

AuthorChristian Stratowa, Vienna, Austria
Bioconductor views DataImport DifferentialExpression ExonArray GeneExpression Microarray OneChannel Preprocessing Transcription
MaintainerChristian Stratowa <[email protected]>
LicenseGPL (>= 2.0)
Version1.37.1
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("Bioconductor-mirror/xps")
Bioconductor-mirror/xps documentation built on June 1, 2017, 8:13 p.m.