A "corrective make-up" program for microarray chips

Bioconductor version: 2.9

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 rockefeller.edu>

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PDF R Script Harshlight
PDF   Reference Manual


biocViews Microarray, QualityControl, Preprocessing, AffymetrixChip, ReportWriting
Depends R (>= 2.1.1)
Imports affy, altcdfenvs, Biobase, stats, utils
System Requirements
License GPL (>= 2)
URL http://asterion.rockefeller.edu/Harshlight/
Depends On Me
Imports Me
Suggests Me
Version 1.26.0
Since Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source Harshlight_1.26.0.tar.gz
Windows Binary Harshlight_1.26.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Harshlight_1.26.0.tgz
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Fred Hutchinson Cancer Research Center