affyPLM

Methods for fitting probe-level models

Bioconductor version: Release (2.11)

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, Software
Version	1.34.0
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	RefPlus
Imports Me	affyQCReport, arrayQualityMetrics, virtualArray
Suggests Me	AffyExpress, affylmGUI, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, frmaTools, ggbio, metahdep, oneChannelGUI

Package Downloads

Package Source	affyPLM_1.34.0.tar.gz
Windows Binary	affyPLM_1.34.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard)	affyPLM_1.34.0.tgz
Package Downloads Report	Download Stats

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