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arrayMvout
multivariate outlier detection for expression array QA
Bioconductor version: 3.0
This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate
Author: Z. Gao, A. Asare, R. Wang, V. Carey
Maintainer: V. Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("arrayMvout")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("arrayMvout")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("arrayMvout")
| R Script | arrayMvout -- multivariate outlier algorithm for expression arrays | |
| Reference Manual |
Details
| biocViews | Infrastructure, Microarray, QualityControl, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) |
| License | Artistic-2.0 |
| Depends | R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi |
| Imports | simpleaffy, mdqc, affyContam |
| LinkingTo | |
| Suggests | MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | arrayMvout_1.24.0.tar.gz |
| Windows Binary | arrayMvout_1.24.0.zip |
| Mac OS X 10.6 (Snow Leopard) | arrayMvout_1.24.0.tgz |
| Mac OS X 10.9 (Mavericks) | arrayMvout_1.24.0.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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