Harshlight

A "corrective make-up" program for microarray chips

Bioconductor version: Release (2.7)

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

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("Harshlight")    

Documentation

PDF

R Script

Harshlight

Reference Manual

Details

biocViews	Microarray, QualityControl, Preprocessing, AffymetrixChip, ReportWriting
Depends	R
Imports	affy, altcdfenvs, Biobase, stats, utils
Suggests
System Requirements
License	GPL (>= 2)
URL	http://asterion.rockefeller.edu/Harshlight/
Depends On Me
Imports Me
Suggests Me
Version	1.20.0

Package Downloads

Package Source	Harshlight_1.20.0.tar.gz
Windows Binary	Harshlight_1.20.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Harshlight_1.20.0.tgz
Package Downloads Report	Download Stats