Harshlight: A "corrective make-up" program for microarray chips
Version 1.48.0

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.

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AuthorMayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco
Bioconductor views Microarray OneChannel Preprocessing QualityControl ReportWriting
Date of publicationNone
MaintainerMaurizio Pellegrino <mpellegri@berkeley.edu>
LicenseGPL (>= 2)
Version1.48.0
URL http://asterion.rockefeller.edu/Harshlight/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Harshlight")

Man pages

HarshComp: a blemish detection program for microarray chips: extended...
HarshExt: a blemish detection program for microarray chips: extended...
Harshlight: a blemish detection program for microarray chips: extended,...
sim: blemish simulations from 100.000 random chips

Functions

AnalyzeChip Source code
CheckParam Source code
ClusterDefects Source code
ClusterNumber Source code
Contiguity Source code
ErrorIntensity Source code
FindCompact Source code
FindDiffuse Source code
FindExtended Source code
GetBound Source code
HarshComp Man page Source code
HarshExt Man page Source code
Harshlight Man page Source code
ImageClose Source code
RetrievePvalues Source code
RetrievePvalues_exact Source code
ScaleErr Source code
ScaleInt Source code
a Man page
b Man page
sim Man page
sim.int Man page
simulations Man page

Files

DESCRIPTION
NAMESPACE
R
R/Harshlight.R
build
build/vignette.rds
data
data/sim.int.rda
data/sim.rda
inst
inst/doc
inst/doc/Harshlight.R
inst/doc/Harshlight.Rnw
inst/doc/Harshlight.pdf
man
man/HarshComp.Rd
man/HarshExt.Rd
man/Harshlight.Rd
man/sim.Rd
src
src/Harshlight.c
vignettes
vignettes/Harshlight.Rnw
Harshlight documentation built on May 20, 2017, 10:18 p.m.