- Home
- Bioconductor 3.4
- Software Packages
- affyPLM
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("affyPLM")
In most cases, you don't need to download the package archive at all.
affyPLM
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see affyPLM.
Methods for fitting probe-level models
Bioconductor version: 3.4
A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
Author: Ben Bolstad <bmb at bmbolstad.com>
Maintainer: Ben Bolstad <bmb at bmbolstad.com>
Citation (from within R,
enter citation("affyPLM")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("affyPLM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("affyPLM")
| R Script | affyPLM: Advanced use of the MAplot function | |
| R Script | affyPLM: Fitting Probe Level Models | |
| R Script | affyPLM: Model Based QC Assessment of Affymetrix GeneChips | |
| R Script | affyPLM: the threestep function | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 1.50.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 12 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.6.0), BiocGenerics(>= 0.3.2), affy(>= 1.11.0), Biobase(>= 2.17.8), gcrma, stats, preprocessCore(>= 1.5.1) |
| Imports | zlibbioc, graphics, grDevices, methods |
| LinkingTo | preprocessCore |
| Suggests | affydata, MASS |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/bmbolstad/affyPLM |
| Depends On Me | RefPlus |
| Imports Me | affylmGUI, affyQCReport, arrayQualityMetrics |
| Suggests Me | AffyExpress, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, ELBOW, frmaTools, metahdep, oneChannelGUI, piano |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | affyPLM_1.50.0.tar.gz |
| Windows Binary | affyPLM_1.50.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | affyPLM_1.50.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/affyPLM/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/affyPLM/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
