The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon array systems (Exon 1.0 ST: core, extended, full probesets) and gene array systems (Gene 1.0 ST) 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, DABG-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.
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("xps")
| Source | xps_1.0.2.tar.gz |
|---|---|
| Windows binary | xps_1.0.2.zip |
| OS X binary | xps_1.0.2.tgz |
| biocViews | |
|---|---|
| Depends | R, methods |
| Suggests | |
| Imports | |
| SystemRequirements | ROOT <http://root.cern.ch> - See README file for installation instructions. |
| License | GPL version 2 or newer |
| URL | |
| dependsOnMe | |
| suggestsMe |