affyPLM

Methods for fitting probe-level models

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
Maintainer	Ben Bolstad

To install this package, start R and enter:

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

Documentation

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

Details

biocViews	Microarray , OneChannel , Preprocessing , QualityControl
Depends	R , affy , Biobase , methods , gcrma , stats , preprocessCore
Imports
Suggests	affydata
System Requirements
License	GPL version 2 or newer
URL	http://bmbolstad.com
Depends On Me	affyQCReport , arrayQualityMetrics , RefPlus
Imports Me
Suggests Me	AffyExpress , affylmGUI , arrayMvout , ArrayTools , BiocCaseStudies , metahdep , oneChannelGUI
Development History	Bioconductor Changelog

Package Downloads

Package source	affyPLM_1.20.0.tar.gz
Windows binary	affyPLM_1.20.0.zip
MacOS X 10.4 (Tiger) binary	affyPLM_1.20.0.tgz
MacOS X 10.5 (Leopard) binary	affyPLM_1.20.0.tgz
Package Downloads Report	Downloads Stats