affyPLM

Methods for fitting probe-level models

Bioconductor version: Development (3.0)

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 1.41.0
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, ELBOW, frmaTools, metahdep, oneChannelGUI, piano

Package Downloads

Package Source affyPLM_1.41.0.tar.gz
Windows Binary affyPLM_1.41.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) affyPLM_1.41.0.tgz
Mac OS X 10.9 (Mavericks)
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