affyPLM

This is the released version of affyPLM; for the devel version, see affyPLM.

Methods for fitting probe-level models

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DOI: 10.18129/B9.bioc.affyPLM

Bioconductor version: Release (3.22)

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 "4.5") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software

Version 1.86.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20.5 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 graphics, grDevices, methods

System Requirements

URL https://github.com/bmbolstad/affyPLM

Suggests affydata, MASS, hgu95av2cdf

Linking To preprocessCore

Enhances

Depends On Me bapred

Imports Me affylmGUI, mimager

Suggests Me arrayMvout, BiocGenerics, frmaTools, metahdep, piano, aroma.affymetrix

Links To Me

Build Report Build Report

Package Archives

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

Source Package affyPLM_1.86.0.tar.gz

Windows Binary (x86_64) affyPLM_1.86.0.zip (64-bit only)

macOS Binary (x86_64) affyPLM_1.86.0.tgz

macOS Binary (arm64) affyPLM_1.86.0.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/

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