Hedenfalk {Equalden.HD}

Hedenfalk data

Description

These data come from the breast cancer gene expression study of Hedenfalk et al. (2001). The data set consists on 3226 gene expression levels measured on 7 patients with breast tumors having BRCA1 mutations (columns 1-7) and on 8 patients with breast tumors having BRCA2 mutations (columns 8-15). The rows correspond to the genes and the columns refer to the patients.

Usage

data(Hedenfalk)

Format

A matrix with 3226 rows corresponding to the measured genes and 15 columns corresponding to the patients. The first 7 columns contain the measures for the patients with BRCA1 mutations and the patients with BRCA2 mutations are located in the last 8 columns.

Source

http://genomine.org/qvalue/results.txt

References

Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M, Bitter, M., Simon, R., Meltzer, P., Guterson, B., Esteller, M., Kallioniemi, O., Wilfond, B., Borg, A., Trent, J., Raffeld, M., Yakhini, Z., BenDor, A., Dougherty, E., Kononen, J., Buberdorf, L., Fehrle, W., Pittaluga, S., Gruvberger, G., Loman, N., Johannsson, O., Olsson, H., and Sauter, G.(2001), Gene-Expression Profiles in Hereditary Breast Cancer. New England Journal of Medicine 344 (8), 539-548.

Examples

data(Hedenfalk)
X <- Hedenfalk
k <- dim(X)[1]
### Estimated densities of logged gene expression levels for patients with BRCA1 mutations.
s <- apply(X[, 1:7], 1, density)
### Plot of estimated densities of 6 randomly selected genes.
set.seed(375)
rs <- sample(1:k, 6)
plot(s[[rs[1]]], main = "Kernel estimates for 6 randomly selected genes",
 xlab = "x", ylab = "density", xlim = c(-1, 4.3), ylim = c(0, 2))
for (i in 2:6){
  lines(s[[rs[i]]], col = i)
}