Package: Harshlight 1.79.0

Maurizio Pellegrino

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.

Authors:Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco

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Harshlight.pdf |Harshlight.html✨
Harshlight/json (API)

# Install 'Harshlight' in R:
install.packages('Harshlight', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • sim - Blemish simulations from 100.000 random chips
  • sim.int - Blemish simulations from 100.000 random chips

On BioConductor:Harshlight-1.79.0(bioc 3.21)Harshlight-1.78.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarrayqualitycontrolpreprocessingonechannelreportwriting

4.20 score 2 scripts 418 downloads 8 mentions 3 exports 27 dependencies

Last updated 4 months agofrom:ed62604b49. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 18 2025
R-4.5-win-x86_64WARNINGFeb 18 2025
R-4.5-linux-x86_64WARNINGFeb 18 2025
R-4.4-win-x86_64WARNINGFeb 18 2025
R-4.4-mac-x86_64WARNINGFeb 18 2025
R-4.4-mac-aarch64WARNINGFeb 18 2025
R-4.3-win-x86_64WARNINGFeb 18 2025
R-4.3-mac-x86_64WARNINGFeb 18 2025
R-4.3-mac-aarch64WARNINGFeb 18 2025

Exports:HarshCompHarshExtHarshlight

Dependencies:affyaffyioaltcdfenvsaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagraphhttrhypergraphIRangesjsonlitemakecdfenvmimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVector

Harshlight

Rendered fromHarshlight.Rnwusingutils::Sweaveon Feb 18 2025.

Last update: 2013-11-01
Started: 2013-11-01