colon: Gene expression data from colon-cancer patients

In biglasso: Extending Lasso Model Fitting to Big Data

Gene expression data from colon-cancer patients

Description

The data file contains gene expression data of 62 samples (40 tumor samples, 22 normal samples) from colon-cancer patients analyzed with an Affymetrix oligonucleotide Hum6000 array.

Format

A list of 2 variables included in colon:

• X: a 62-by-2000 matrix that records the gene expression data. Used as design matrix.

• y: a binary vector of length 62 recording the sample status: 1 = tumor; 0 = normal. Used as response vector.

Source

The raw data can be found on Bioconductor: https://bioconductor.org/packages/release/data/experiment/html/colonCA.html.

References

• U. Alon et al. (1999): Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissue probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96, 6745-6750. https://www.pnas.org/doi/abs/10.1073/pnas.96.12.6745.

Examples

data(colon)
X <- colon$X
y <- colon$y
str(X)
dim(X)
X.bm <- as.big.matrix(X, backingfile = "") # convert to big.matrix object
str(X.bm)
dim(X.bm)

biglasso documentation built on May 29, 2024, 1:50 a.m.