affyPLM

Methods for fitting probe-level models

Bioconductor version: 2.7

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 arrayQualityMetrics, frma, frmaTools, RefPlus
Imports Me affyQCReport, frma
Suggests Me AffyExpress, affylmGUI, arrayMvout, ArrayTools, BiocCaseStudies, frmaTools, metahdep, oneChannelGUI
Version 1.26.1
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source affyPLM_1.26.1.tar.gz
Windows Binary affyPLM_1.26.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary affyPLM_1.26.1.tgz
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