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Methods for fitting probe-level models

Bioconductor version: Release (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>

Maintainer: Ben Bolstad <bmb at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 1.80.0
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
See More
Suggests affydata, MASS, hgu95av2cdf
Linking To preprocessCore
Depends On Me bapred
Imports Me affylmGUI, arrayQualityMetrics, 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_1.80.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) affyPLM_1.80.0.tgz
macOS Binary (arm64) affyPLM_1.80.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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