affyPLM
Methods for fitting probe-level models
Bioconductor version: 3.23 · Package version: 1.88.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("affyPLM")Details
| Maintainer | Ben Bolstad <bmb@bmbolstad.com> |
| Author | Ben Bolstad <bmb@bmbolstad.com> |
| License | GPL (>= 2) |
| URL | https://github.com/bmbolstad/affyPLM |
| Downloads rank | 1934 |
| Source branch | RELEASE_3_23 |
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
Documentation
- affyPLM: Advanced use of the MAplot function
- affyPLM: Fitting Probe Level Models
- affyPLM: Model Based QC Assessment of Affymetrix GeneChips
- affyPLM: the threestep function
Download
Follow the installation instructions to use this package in your R session.
| Source package | affyPLM_1.88.0.tar.gz |
| Windows binary (x86_64) | affyPLM_1.88.0.zip |
| macOS binary (arm64) | affyPLM_1.88.0.tgz |
| macOS binary (x86_64) | affyPLM_1.88.0.tgz |
Dependencies
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
LinkingTo: preprocessCore
Suggests: affydata, MASS, hgu95av2cdf
Reverse dependencies
Depends On Me (1): bapred
Imports Me (3): affylmGUI, arrayQualityMetrics, mimager
Suggests Me (5): aroma.affymetrix, arrayMvout, BiocGenerics, frmaTools, piano