Harshlight

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Harshlight.

A "corrective make-up" program for microarray chips

Bioconductor version: 3.9

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 berkeley.edu>

Citation (from within R, enter citation("Harshlight")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Harshlight")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Harshlight")

Harshlight	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software
Version	1.56.0
In Bioconductor since	BioC 1.9 (R-2.4) (17.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10)
Imports	affy, altcdfenvs, Biobase, stats, utils
System Requirements
URL	http://asterion.rockefeller.edu/Harshlight/

Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Harshlight_1.56.0.tar.gz
Windows Binary	Harshlight_1.56.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Harshlight_1.56.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Harshlight
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Harshlight
Bioc Package Browser	https://code.bioconductor.org/browse/Harshlight/
Package Short Url	https://bioconductor.org/packages/Harshlight/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive