Real.2: Real Dataset #2: Genomic Dataset ($p >> n$ case)
Description
Publicly available lung cancer data from the Chemores Cohort Study. This was an integrated study of mRNA, miRNA
and clinical variables to characterize the molecular distinctions between squamous cell carcinoma (SCC) and adenocarcinoma (AC)
in Non Small Cell Lung Cancer (NSCLC). Tissue samples were analysed from a cohort of 123 patients who underwent complete
surgical resection at the Institut Mutualiste Montsouris (Paris, France) between 30 January 2002 and 26 June 2006.
In this genomic dataset, only the expression levels of Agilent miRNA probes ($p=939$) were included from the $n=123$
samples of the Chemores cohort. The data contains normalized expression levels. See below the paper by Lazar et al. (2013)
and Array Express data repository for complete description of the samples, tissue preparation,
Agilent array technology, data normalization, etc. This dataset represents a situation where the number of covariates dominates
the number of complete observations, or $p >> n$ case.format
Dataset consists of a numeric data.frame containing $n=123$ complete observations (samples)
by rows and $p=939$ genomic covariates by columns, not including the censoring indicator and (censored) time-to-event variables.
It comes as a compressed Rda data file.source
See real data application in Dazard et al., 2015.References
- Dazard J-E., Choe M., LeBlanc M. and Rao J.S. (2015).
"Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods."
(Submitted).
- Dazard J-E., Choe M., LeBlanc M. and Rao J.S. (2014).
"Cross-Validation of Survival Bump Hunting by Recursive Peeling Methods."
In JSM Proceedings, Survival Methods for Risk Estimation/Prediction Section. Boston, MA, USA.
American Statistical Association IMS - JSM, p. 3366-3380.
- Dazard J-E. and J. S. Rao (2010).
"Local Sparse Bump Hunting."
J. Comp Graph. Statistics, 19(4):900-92.
- Lazar V. et al. (2013).
"Integrated molecular portrait of non-small cell lung cancers.BMC Medical Genomics 6:53-65. PMID: 24299561
See Also
Array Express data repository at the European Bioinformatics Institute.
Accession number: #E-MTAB-1134 (MIR).www.ebi.ac.uk/arrayexpress/
CHEMORES Consortium and website.http://www.chemores.ki.se/index.html