- Home
- Bioconductor 2.8
- Software Packages
- Harshlight
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harshlight")
In most cases, you don't need to download the package archive at all.
Harshlight
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see Harshlight.
A "corrective make-up" program for microarray chips
Bioconductor version: 2.8
The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.
Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco
Maintainer: Maurizio Pellegrino <mpellegri at rockefeller.edu>
Citation (from within R,
enter citation("Harshlight")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harshlight")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Harshlight")
| Harshlight.pdf | ||
| Reference Manual |
Details
| biocViews | AffymetrixChip, Microarray, Preprocessing, QualityControl, ReportWriting, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 1.9 (R-2.4) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.1.1) |
| Imports | affy, altcdfenvs, Biobase, stats, utils |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://asterion.rockefeller.edu/Harshlight/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Harshlight_1.24.0.tar.gz |
| Windows Binary | Harshlight_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/Harshlight/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/Harshlight/ |
| 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
