MVR (version 1.20.0)

Real: Real Proteomics Dataset

Description

The dataset comes from a quantitative Liquid Chromatography/Mass-Spectrometry (LC/MS) shotgun (bottom-up) proteomics experiment. It consists of $n=6$ independent cell cultures of human of Myeloid Dendritic Cells (MDCs) from normal subjects. Samples were split into a control ("M") and a treated group ("S"), stimulated with either media alone or a Toll-Like receptor-3 Ligand respectively. The goal was to identify differentially expressed peptides (or proteins) between the two groups involved in the immune response of human MDCs upon TLR-3 Ligand binding. The dataset is assumed to have been pre-processed for non-ignorable missing values, leaving a complete dataset with $p=9052$ unique peptides or predictor variables. This is a balanced design with two sample groups ($G=2$), under unequal sample group variance.

Usage

Real

format

A numeric matrix containing $n=6$ observations (samples) by rows and $p=9052$ variables by columns, named after peptide names ($diffset_{1}, ..., diffset_{p}$). Samples are balanced ($n_{1}=3$,$n_{2}=3$) between the two groups ("M", "S"). Compressed Rda data file.

source

See real proteomics data application in Dazard et al., 2011, 2012.

References

• Dazard J-E., Hua Xu and J. S. Rao (2011). "R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization." In JSM Proceedings, Section for Statistical Programmers and Analysts. Miami Beach, FL, USA: American Statistical Association IMS - JSM, 3849-3863.
• Dazard J-E. and J. S. Rao (2012). "Joint Adaptive Mean-Variance Regularization and Variance Stabilization of High Dimensional Data." Comput. Statist. Data Anal. 56(7):2317-2333.