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The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization

Metadata Updated: August 20, 2021

This dataset is a project file generated by BMDExpress 2.2 SW (Sciome, Research Triangle Park, NC). It contains gene expression data for livers of rats exposed to 4 chemicals (crude MCHM, neat MCHM, DMPT, p-toluidine) and kidneys of rats exposed to PPH. The project file includes normalized expression data (GeneChip Rat 230 2.0 Array) using 7 different pre-processing methods (RMA, GCRMA, MAS5.0, MAS5.0_noA calls, PLIER, PLIER16, and PLIER16_noA calls); differentially expressed probe-sets detected by William's method (p<0.05, and minimum fold change of 1.5); probeset-level and pathway-level BMD and BMDL values from transcriptomic dose-response modeling.

This dataset is associated with the following publication: Mezencev, R., and S. Auerbach. The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PLOS ONE. Public Library of Science, San Francisco, CA, USA, 15(5): e0232955, (2020).

Access & Use Information

Public: This dataset is intended for public access and use. License: See this page for license information.

Downloads & Resources

References

https://doi.org/10.1371/journal.pone.0232955

Dates

Metadata Created Date August 20, 2021
Metadata Updated Date August 20, 2021

Metadata Source

Harvested from EPA ScienceHub

Additional Metadata

Resource Type Dataset
Metadata Created Date August 20, 2021
Metadata Updated Date August 20, 2021
Publisher U.S. EPA Office of Research and Development (ORD)
Maintainer
Identifier https://doi.org/10.23719/1504295
Data Last Modified 2018-08-30
Public Access Level public
Bureau Code 020:00
Schema Version https://project-open-data.cio.gov/v1.1/schema
Data Dictionary https://pasteur.epa.gov/uploads/10.23719/1504295/documents/Mezencev_Auerbach_Data_Dictionary.docx
Data Dictionary Type application/vnd.openxmlformats-officedocument.wordprocessingml.document
Harvest Object Id 31341861-2266-4b04-b27e-63aee6b4804d
Harvest Source Id 04b59eaf-ae53-4066-93db-80f2ed0df446
Harvest Source Title EPA ScienceHub
License https://pasteur.epa.gov/license/sciencehub-license.html
Program Code 020:062
Publisher Hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
Related Documents https://doi.org/10.1371/journal.pone.0232955
Source Datajson Identifier True
Source Hash eea4d02398f85c7d708407f99a3f9639ad06ec63
Source Schema Version 1.1

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