To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PAA")
In most cases, you don't need to download the package archive at all.
PAA
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see PAA.
PAA (Protein Array Analyzer)
Bioconductor version: 3.4
PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.
Author: Michael Turewicz [aut, cre], Martin Eisenacher [ctb, cre]
Maintainer: Michael Turewicz <michael.turewicz at rub.de>, Martin Eisenacher <martin.eisenacher at rub.de>
Citation (from within R,
enter citation("PAA")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PAA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PAA")
| R Script | PAA tutorial | |
| PAA_1.7.1.pdf | ||
| Reference Manual | ||
| Text | README | |
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Classification, Microarray, OneChannel, Proteomics, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 3.2.0), Rcpp (>= 0.11.6) |
| Imports | e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva |
| LinkingTo | Rcpp |
| Suggests | BiocStyle, RUnit, BiocGenerics, vsn |
| SystemRequirements | C++ software package Random Jungle |
| Enhances | |
| URL | http://www.ruhr-uni-bochum.de/mpc/software/PAA/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PAA_1.8.0.tar.gz |
| Windows Binary | PAA_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | PAA_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PAA/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/PAA/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
