source("http://bioconductor.org/biocLite.R")
biocLite("affyPLM")

affyPLM

Methods for fitting probe-level models

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

source("http://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")

 

PDF	R Script	affyPLM: Advanced use of the MAplot function
PDF	R Script	affyPLM: Fitting Probe Level Models
PDF	R Script	affyPLM: Model Based QC Assessment of Affymetrix GeneChips
PDF	R Script	affyPLM: the threestep function
PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, QualityControl, Software
Version	1.38.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier
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	BiocGenerics, zlibbioc, graphics, grDevices, methods
Suggests	affydata, MASS
System Requirements
URL	http://bmbolstad.com
Depends On Me	affylmGUI, affylmGUI, RefPlus
Imports Me	affyQCReport, arrayQualityMetrics, virtualArray
Suggests Me	AffyExpress, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, frmaTools, ggbio, metahdep, oneChannelGUI, piano

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	affyPLM_1.38.0.tar.gz
Windows Binary	affyPLM_1.38.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	affyPLM_1.38.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats