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Bioconductor - affyPLM (development version)

affyPLM

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

Methods for fitting probe-level models

Bioconductor version: Development (3.22)

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")

# 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 1.85.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20 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 See More Package Archives

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

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