Harshlight protocols

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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

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Publication for Harshlight

Harshlight in pipelines

 (3)
2015
PMCID: 4406155
PMID: 25512250
DOI: 10.1002/art.38995

[…] on the arthritis & rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.38995/abstract) as previously described ()., 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 […]

2012
PMCID: 3352975
PMID: 22402443
DOI: 10.1038/jid.2012.33

[…] standard procedures were used. antibodies used in this experiment are listed in ., microarray data was analyzed using genespring gx version10.0 software (agilent) and r/bioconductor packages. the harshlight package () was used to scan affymetrix chips for spatial artifacts. expression values were obtained using the rma procedure. expression values were modeled using the mixed-effect framework […]

2011
PMCID: 3235105
PMID: 22174793
DOI: 10.1371/journal.pone.0028358

[…] were employed to evaluate the quality of the arrays by means of images, histograms, box plots, degradation plots, and scatter plots. cel files were scrutinized for spatial artifacts using harshlight package (pmc1274260). using the median value of a group of replicates as the reference value, we corrected a small blemish affecting the readings for one of the whole-embryo control […]


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Harshlight in publications

 (17)
PMCID: 5259951
PMID: 28155655
DOI: 10.1186/s12864-016-3319-5

[…] 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 [] […]

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

[…] st-louis, mo)., 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 […]

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

[…] ecgs throughout the study., 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 […]

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 […]

PMCID: 4505786
PMID: 26236467
DOI: 10.5256/f1000research.7066.r9426

[…] 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 […]


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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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