DEGraph (version 1.24.0)

exprLoi2008: Gene expression data used in the DEGraph package vignette

Description

This data set gives gene expression data for a subset of 227 genes used in the DEGraph package vignette. This comes from the 15737 gene, 255 patient dataset of Loi et al. (2008) which was used to study resistance to tamoxifen treatment in hormone-dependent breast cancer.

Usage

exprLoi2008

Format

A matrix of 227 lines and 255 columns.

Source

Loi et al., Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9(1):239, 2008.

Details

The original data set corresponds to data processed by RMA and median-centered as available from the GSE6532 GEO archive: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532. These data were summarized from the probe set level to the gene level as follows. The expression level of a gene was defined as the expression level of the probe set with largest alignment score among all probe sets mapping to this gene according to the annotation in GSE6532. When the largest alignment score was achieved by several probe sets, the median expression level of those probe sets was taken.

References

Loi et al., Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9(1):239, 2008.

Examples

data("Loi2008_DEGraphVignette")

dim(exprLoi2008)
head(exprLoi2008)