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>

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

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

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