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Harshlight specifications

Information


Unique identifier OMICS_02001
Name Harshlight
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.52.0
Stability Stable
Requirements
stats, Biobase, utils, R(>=2.10), affy, altcdfenvs
Maintained Yes

Versioning


No version available

Documentation


Publication for Harshlight

Harshlight citations

 (18)
library_books

Between species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

2016
BMC Genomics
PMCID: 5259951
PMID: 28155655
DOI: 10.1186/s12864-016-3319-5

[…] to R (version 2.14.1). One of the A. halleri gDNA hybridizations (Mw_101105_03X.CEL) was detected to have some compact defects affecting nearly 2% of the total probes. This defect was corrected using Harshlight package in R [], wherein the corresponding probe signal of the replicate GeneChip replaced the values of erroneous probes. We used the affy [] and VSN2 [] package to apply MAS5.0 [] backgro […]

library_books

Based on Molecular Profiling of Gene Expression, Palmoplantar Pustulosis and Palmoplantar Pustular Psoriasis Are Highly Related Diseases that Appear to Be Distinct from Psoriasis Vulgaris

2016
PLoS One
PMCID: 4859542
PMID: 27152848
DOI: 10.1371/journal.pone.0155215

[…] Quality control of microarray chips was carried out using standard QC metrics and R package microarray Quality Control. Images were scrutinized for spatial artifacts using Harshlight. Expression measures were obtained using the RMA algorithm with an extra loess-normalization step. Since normal non-acral-skin chips where hybridized in a different batch, we took several s […]

library_books

A Randomized, Placebo Controlled Study of SRT2104, a SIRT1 Activator, in Patients with Moderate to Severe Psoriasis

2015
PLoS One
PMCID: 4640558
PMID: 26556603
DOI: 10.1371/journal.pone.0142081

[…] Quality control of microarray chips was carried out using standard QC metrics and R package microarray Quality Control Images were scrutinized for spatial artifacts using Harshlight []. Expression measures were obtained using GCRMA algorithm []. Probe-sets with at least one sample with expression values larger than 4 and standard deviation (SD)>0.1 were kept for furthe […]

library_books

Integrated network analysis and logistic regression modeling identify stage specific genes in Oral Squamous Cell Carcinoma

2015
BMC Med Genomics
PMCID: 4502639
PMID: 26179909
DOI: 10.1186/s12920-015-0114-0

[…] processed using affy package. At initial levels of quality control (QC), all samples were pre-processed together using the standard affyQCReport and affyPLM quality assessment software packages. The Harshlight package [] was utilized to remove the effects of spatial blemishes. As a general principle, chips with extensive defects were eliminated from the datasets. Background correction, quantile n […]

call_split

Psoriasis is characterized by deficient negative immune regulation compared to transient delayed type hypersensitivity reactions

2015
F1000Res
PMCID: 4505786
PMID: 26236467
DOI: 10.5256/f1000research.7066.r9426
call_split See protocol

[…] 33 Plus 2.0 chips (Affymetrix, Santa Clara, CA) to measure relative gene expression. Statistical analysis. Microarray data were analyzed using R/Bioconductor packages ( http://www.r-project.org). The Harshlight package was used to scan Affymetrix chips for spatial artifacts. Expression values were normalized using the GeneChip Robust Multi-array Average (GCRMA) algorithm. Genes with low variation […]

library_books

Comparative Genomic Profiling of Synovium Versus Skin Lesions in Psoriatic Arthritis

2015
PMCID: 4406155
PMID: 25512250
DOI: 10.1002/art.38995

[…] Quality control of microarray data was conducted using a Harshlight package (http://asterion.rockefeller.edu/Harshlight/index2.html) () and ArrayQuality Control packages in R (http://www.r-project.org/). A GC-RMA algorithm was used to calculate expression v […]

Citations

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Harshlight institution(s)
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA

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