Harshlight

DOI: 10.18129/B9.bioc.Harshlight    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Harshlight.

A "corrective make-up" program for microarray chips

Bioconductor version: 3.8

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 berkeley.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Harshlight
PDF		Reference Manual

Details

biocViews	Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software
Version	1.54.0
In Bioconductor since	BioC 1.9 (R-2.4) (12.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10)
Imports	affy, altcdfenvs, Biobase, stats, utils
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URL	http://asterion.rockefeller.edu/Harshlight/
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Package Archives

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

Source Package	Harshlight_1.54.0.tar.gz
Windows Binary	Harshlight_1.54.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Harshlight_1.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Harshlight
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Harshlight
Package Short Url	http://bioconductor.org/packages/Harshlight/
Package Downloads Report	Download Stats