This data set consists of gene expression and DNA copy number measurements on a set of 89 samples. The data set can be used to perform integrative analysis of gene expression and DNA copy number data, as in . That is, we can look for sets of genes that are associated with regions of chromosomal gain/loss.
Must be downloaded from https://statweb.stanford.edu/~tibs/PMA/ and put into the folder PMA/data
The format is a list containing the following elements: - dna: a 2149x89 matrix of CGH spots x Samples - rna: a 19672x89 matrix of Genes x Samples - chrom: a 2149-vector of chromosomal location of each CGH spot - nuc: a 2149-vector of nucleotide position for each CGH spot - gene: a 19672-vector wiith an accession number for each gene - genenames: a 19672-vector with a name for each gene - genechr: a 19672-vector with a chromosomal location for each gene - genedesc: a 19672-vector with a description for each gene - genepos: a 19672-vector with a nucleotide position for each gene
Missing values were imputed using 5-nearest neighbors (see library
Chin K., et. al. (2006) doi: 10.1016/j.ccr.2006.10.009.
Witten D. M., Tibshirani R., and Hastie, T. (2009) doi: 10.1093/biostatistics/kxp008.
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