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Harshlight

A "corrective make-up" program for microarray chips


Bioconductor version: Release (3.19)

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 "4.4") 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

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software
Version 1.76.0
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/
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Package Archives

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

Source Package Harshlight_1.76.0.tar.gz
Windows Binary Harshlight_1.76.0.zip (64-bit only)
macOS Binary (x86_64) Harshlight_1.76.0.tgz
macOS Binary (arm64) Harshlight_1.76.0.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/
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