AffyProbeMiner specifications

Information


Unique identifier OMICS_26694
Name AffyProbeMiner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Hongfang Liu <>
  • person_outline Barry Zeeberg <>

Publication for AffyProbeMiner

AffyProbeMiner in publications

 (19)
PMCID: 5883543
PMID: 29614978
DOI: 10.1186/s12885-018-4103-5

[…] probes mapping to more than one gene were excluded. the output file from spliceminer and the ht hg-u133a chip definition file (cdf) were passed to the alternate cdf-generating function makealtcdf of affyprobeminer []. probe sets with less than five probes were excluded from the resulting alternative cdf, which was then converted to an r package using makecdfenv. the cdf was used to perform […]

PMCID: 5755453
PMID: 29301495
DOI: 10.1186/s12865-017-0238-4

[…] 395 infected samples (e.coli, t.congolense, m.avium, m.bovis, salmonella and s.aureus) and 212 control samples (table ). microarray probe-sets were mapped to bos taurus umd 3.1 genome assembly using affyprobeminer [] with december 2014 release of bos taurus genome annotation [] as reference. probe-set ids with no mapped entrez gene id or probe-set ids that mapped to more than one entrez gene id […]

PMCID: 5094014
PMID: 27806696
DOI: 10.1186/s12864-016-3176-2

[…] of the affymetrix genechip bovine genome array was obtained from the gpl2112 microarray platform (august 2014) []. microarray probe sets were mapped to bos taurus umd 3.1.1 genome assembly using affyprobeminer [] with december 2014 release of bos taurus genome annotation as reference []. the control probes from the affymetrix genechip bovine genome array were removed from the sample data. […]

PMCID: 4595991
PMID: 26504573
DOI: 10.1038/hortres.2015.26

[…] also some protein–protein interaction (ppi) networks, but these networks were inferred based on ppi networks of arabidopsis., in this study, we first made a customized chip definition file (cdf) by affyprobeminer to transfer probes to gene locus. then, seven gene coexpression networks were constructed by rmtgenenet using all or part of 230 citrus microarrays. these networks were partitioned […]

PMCID: 4309725
PMID: 25622900
DOI: 10.1016/j.neo.2014.11.003

[…] he died a very long time after the diagnostic. raw data in cel files are publicly available and were processed according to the method defined by pierre et al., by using alternative cdfs from affyprobeminer and gcrma for normalization and summarization of downloaded data in the r statistical environment . kaplan-meier curves were drawn with graphpad prism using disease-specific survival […]


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AffyProbeMiner institution(s)
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC, USA; Electrical & Computer Engineering and Institute for Advanced Studies, University of Maryland, College Park, College Park, MD, USA; Department of Information Systems, University of Maryland, Baltimore County, MD, USA; Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, MD, USA; Department of Bioinformatics, George Mason University, Fairfax, VA, USA; Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA; SRA International, Fairfax, VA, USA
AffyProbeMiner funding source(s)
Supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, by NSF grant IIS-0430743, and by the Intramural Research Program of the NIH, Center for Information Technology and the NIH Clinical Center.

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