mammaPrintData

Curated gene expression data from the two breast cancer cohorts used to implement and validate the MammaPrint 70-gene prognostic signature:

• the Glas et al. (2006) implementation study, ArrayExpress E-TABM-115 (162 patients), provided as glasRGcy5 and glasRGcy3;
• the Buyse et al. (2006) TRANSBIG validation study, ArrayExpress E-TABM-77 (307 patients), provided as buyseRGcy5 and buyseRGcy3.

Both cohorts were profiled on the custom two-color Agilent 1.9k MammaPrint array (A-MEXP-318) with a dye-swap design; each data set is a pair of limma RGList objects (one per dye orientation) with probe annotation and clinical information attached. The 70-gene signature itself is available as the seventyGeneSignature data set.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("mammaPrintData")

Usage

library(mammaPrintData)
library(limma)

data(glasRGcy5)
data(seventyGeneSignature)
dim(glasRGcy5)
head(glasRGcy5$targets)
head(seventyGeneSignature)

Raw data

The original ArrayExpress files are no longer bundled with the package. They are archived on Zenodo (doi:10.5281/zenodo.22285418) and served per file by EBI BioStudies; fetchMammaPrintRaw() downloads and caches them from either source. The scripts that regenerate the processed objects live in data-raw/.

The Zenodo record is published under CC-BY-4.0; the ArrayExpress files in it are redistributed under the EMBL-EBI terms of use with attribution to the original studies, and 415530a-s9.xls is archived verbatim from the supplementary material of van 't Veer et al. (2002).