affyPLM

DOI: 10.18129/B9.bioc.affyPLM    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see affyPLM.

Methods for fitting probe-level models

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("affyPLM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("affyPLM")

 

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	1.60.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14.5 years)
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	zlibbioc, graphics, grDevices, methods
LinkingTo	preprocessCore
Suggests	affydata, MASS
SystemRequirements
Enhances
URL	https://github.com/bmbolstad/affyPLM
Depends On Me	RefPlus
Imports Me	affylmGUI, affyQCReport, arrayQualityMetrics, mimager
Suggests Me	AffyExpress, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, ELBOW, frmaTools, metahdep, piano
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	affyPLM_1.60.0.tar.gz
Windows Binary	affyPLM_1.60.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	affyPLM_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/affyPLM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/affyPLM
Package Short Url	https://bioconductor.org/packages/affyPLM/
Package Downloads Report	Download Stats