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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("affyPLM")
In most cases, you don't need to download the package archive at all.
affyPLM
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Methods for fitting probe-level models
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("affyPLM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("affyPLM")
| R Script | affyPLM: Advanced use of the MAplot function | |
| R Script | affyPLM: Fitting Probe Level Models | |
| R Script | affyPLM: Model Based QC Assessment of Affymetrix GeneChips | |
| R Script | affyPLM: the threestep function | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 1.52.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 12.5 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, oneChannelGUI, piano |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | affyPLM_1.52.1.tar.gz |
| Windows Binary | affyPLM_1.52.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | affyPLM_1.52.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/affyPLM |
| Package Short Url | http://bioconductor.org/packages/affyPLM/ |
| Package Downloads Report | Download Stats |
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