colon {sdwd}

simplified gene expression data from Alon et al. (1999)

Description

Gene expression data (2000 genes for 62 samples) from a DNA microarray experiments of colon tissue samples (Alon et al., 1999).

Usage

data(colon)

Details

This data set contains 62 colon tissue samples with 2000 gene expression levels. Among 62 samples, 40 are tumor tissues (coded 1) and 22 are normal tissues (coded -1).

Value

A list with the following elements:

x

A matrix of 2000 columns and 62 rows standing for 2000 gene expression levels and 62 colon tissue samples. Each row corresponds to a patient.

y

A numeric vector of length 62 representing the tissue type (1 for tumor; -1 for normal).

Source

The data were introduced in Alon et al. (1999).

References

Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D., and Levine, A.J. (1999). “Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays”, Proceedings of the National Academy of Sciences, 96(12), 6745–6750.

Examples

# load sdwd library
library(sdwd)

# load data set
data(colon)

# how many samples and how many predictors?
dim(colon$x)

# how many samples of class -1 and 1 respectively?
sum(colon$y == -1)
sum(colon$y == 1)