The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization
Description
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).
Resources
| Name |
Format |
Description |
Link |
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57 |
Mezencev_Auerbach_5_cmpds_7_normalizations_BMDExpress.zip |
https://pasteur.epa.gov/uploads/10.23719/1504295/Mezencev_Auerbach_5_cmpds_7_normalizations_BMDExpress.zip |
Tags
- toxicogenomics
- microarray
- dose-response-modeling