simone (version 0.1-3)

cancer: Microarray data set for breast cancer

Description

This gene expression data set was provided by Hess et al. It concerns one hundred thirty-three patients with stage I--III breast cancer. Patients were treated with chemotherapy prior to surgery. Patient response to the treatment can be classified as either a pathologic complete response (pCR) or residual disease (not-pCR). Hess et al developed and tested a reliable multigene predictor for treatment response on this data set, composed by a set of 26 genes having a high predictive value.

The data set is split into 2 parts (pCR and not pCR), on which network inference algorithms should be applied independently: only individuals from the same classes should be consider as independent and identically distributed.

Usage

data(cancer)

format

cancer.full is a data.frame of the complete data set (133 rows and 26 columns). cancer.pcr is a data.frame of pCR data (34 rows and 26 columns).

cancer.notpcr is a data.frame of not-pCR data (99 rows and 26 columns).

gene.names is a vector of names of the 26 selected genes.

References

Hess, K.R. and Anderson, K. and Symmans, W.F. and Valero, V. and Ibrahim, N. and Mejia, J.A. and Booser, D. and Theriault, R.L. and Buzdar, U. and Dempsey, P.J. and Rouzier, R. and Sneige, N. and Ross, J.S. and Vidaurre, T. and Gomez, H.L. and Hortobagyi, G.N. and Pustzai, L. Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in breast cancer, Journal of Clinical Oncology, 2006, volume 24(26), pages 4236--4244.

Natowicz, R. and Incitti, R. and Horta, E.G. and Charles, B. and Guinot, P. and Yan, K. and Coutant, C. and Andre, F. and Pusztai, L. Rouzier, R. Prediction of the outcome of a preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete response, BMC Bioinformatics, 2008, 9 (149).

Examples

## load simone library and the data set
library(simone)
data(cancer)

## summary of gene expression levels for pCR and not-pCR
summary(cancer.pcr)
summary(cancer.notpcr)