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

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
Date of publication
None
Maintainer
Maurizio Pellegrino <mpellegri@berkeley.edu>
License
GPL (>= 2)
Version
1.46.0
URLs

View on Bioconductor

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

Files in this package

Harshlight/DESCRIPTION
Harshlight/NAMESPACE
Harshlight/R
Harshlight/R/Harshlight.R
Harshlight/build
Harshlight/build/vignette.rds
Harshlight/data
Harshlight/data/sim.int.rda
Harshlight/data/sim.rda
Harshlight/inst
Harshlight/inst/doc
Harshlight/inst/doc/Harshlight.R
Harshlight/inst/doc/Harshlight.Rnw
Harshlight/inst/doc/Harshlight.pdf
Harshlight/man
Harshlight/man/HarshComp.Rd
Harshlight/man/HarshExt.Rd
Harshlight/man/Harshlight.Rd
Harshlight/man/sim.Rd
Harshlight/src
Harshlight/src/Harshlight.c
Harshlight/vignettes
Harshlight/vignettes/Harshlight.Rnw