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This is the development version of Harshlight; for the stable release version, see Harshlight.

A "corrective make-up" program for microarray chips

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

Harshlight PDF R Script
Reference Manual PDF


biocViews Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software
Version 1.77.0
In Bioconductor since BioC 1.9 (R-2.4) (18 years)
License GPL (>= 2)
Depends R (>= 2.10)
Imports affy, altcdfenvs, Biobase, stats, utils
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Source Package Harshlight_1.77.0.tar.gz
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macOS Binary (x86_64) Harshlight_1.77.0.tgz
macOS Binary (arm64) Harshlight_1.77.0.tgz
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