affyPLM

Methods for fitting probe-level models

Bioconductor version: 2.5

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("affyPLM")

Documentation

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
Depends	R (>= 2.6.0), affy(>= 1.11.0), Biobase, methods, gcrma, stats, preprocessCore(>= 1.5.1)
Imports
Suggests	affydata
System Requirements
License	GPL (>= 2)
URL	http://bmbolstad.com
Depends On Me	affyQCReport, arrayQualityMetrics, RefPlus
Imports Me
Suggests Me	AffyExpress, affylmGUI, arrayMvout, ArrayTools, BiocCaseStudies, metahdep, oneChannelGUI
Version	1.22.0
Since	Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source	affyPLM_1.22.0.tar.gz
Windows Binary	affyPLM_1.22.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	affyPLM_1.22.0.tgz
Package Downloads Report	Download Stats

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