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affyPLM

This is the development version of affyPLM; for the stable release version, see affyPLM.

Methods for fitting probe-level models


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("affyPLM")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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 R Script
Reference Manual PDF

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 1.79.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 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
System Requirements
URL https://github.com/bmbolstad/affyPLM
See More
Suggests affydata, MASS, hgu95av2cdf
Linking To preprocessCore
Enhances
Depends On Me RefPlus
Imports Me affylmGUI, arrayQualityMetrics, mimager
Suggests Me arrayMvout, BiocGenerics, frmaTools, metahdep, piano
Links To Me
Build Report Build Report

Package Archives

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

Source Package affyPLM_1.79.0.tar.gz
Windows Binary affyPLM_1.79.0.zip (64-bit only)
macOS Binary (x86_64) affyPLM_1.79.0.tgz
macOS Binary (arm64) affyPLM_1.79.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/affyPLM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/affyPLM
Bioc Package Browser https://code.bioconductor.org/browse/affyPLM/
Package Short Url https://bioconductor.org/packages/affyPLM/
Package Downloads Report Download Stats