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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("affyPLM")
In most cases, you don't need to download the package archive at all.
affyPLM
Methods for fitting probe-level models
Bioconductor version: 3.0
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.
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:
source("http://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 | 1.42.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| 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 | BiocGenerics, zlibbioc, graphics, grDevices, methods |
| LinkingTo | preprocessCore |
| Suggests | affydata, MASS |
| SystemRequirements | |
| Enhances | |
| URL | http://bmbolstad.com |
| Depends On Me | affylmGUI, RefPlus |
| Imports Me | affyQCReport, arrayQualityMetrics |
| 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.
| Package Source | affyPLM_1.42.0.tar.gz |
| Windows Binary | affyPLM_1.42.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | affyPLM_1.42.0.tgz |
| Mac OS X 10.9 (Mavericks) | affyPLM_1.42.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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