affyPLM
This is the development version of affyPLM; for the stable release version, see affyPLM.
Methods for fitting probe-level models
Bioconductor version: Development (3.24)
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("affyPLM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| affyPLM: Fitting Probe Level Models | R Script | |
| affyPLM: Model Based QC Assessment of Affymetrix GeneChips | R Script | |
| affyPLM: the threestep function | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 1.89.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 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
| Suggests | affydata, MASS, hgu95av2cdf |
| Linking To | preprocessCore |
| Enhances | |
| 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_1.89.0.tar.gz |
| Windows Binary (x86_64) | affyPLM_1.89.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | affyPLM_1.89.0.tgz |
| macOS Binary (sonoma-arm64) | affyPLM_1.89.0.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/ |
| Package Downloads Report | Download Stats |