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Harshlight specifications


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
stats, Biobase, utils, R(>=2.10), affy, altcdfenvs
Maintained Yes


No version available


Publication for Harshlight

Harshlight citations


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

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 […]


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

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 […]


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

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 […]


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

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 […]


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

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 […]


Comparative Genomic Profiling of Synovium Versus Skin Lesions in Psoriatic Arthritis

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 […]


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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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