singh2002: Prostate Cancer Study of Singh et al. (2002)

In sda: Shrinkage Discriminant Analysis and CAT Score Variable Selection

Description

Gene expression data (6033 genes for 102 samples) from the microarray study of Singh et al. (2002).

Usage

data(singh2002)

Format

singh2002$x is a 102 x 6033 matrix containing the expression levels. The rows contain the samples and the columns the genes.

singh2002$y is a factor containing the diagnosis for each sample ("cancer" or "healthy").

Details

This data set contains measurements of the gene expression of 6033 genes for 102 observations: 52 prostate cancer patients and 50 healty men.

Source

The data are described in Singh et al. (2001) and are provided in exactly the form as used by Efron (2008).

References

D. Singh et al. 2002. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1:203–209.

Efron, B. 2008. Empirical Bayes estimates for large-scale prediction problems. Technical Report, Standford University.

Examples

# load sda library
library("sda")

# load Singh et al (2001) data set
data(singh2002)
dim(singh2002$x) # 102 6033
hist(singh2002$x)
singh2002$y # 2 levels

Example output

Loading required package: entropy
Loading required package: corpcor
Loading required package: fdrtool
[1]  102 6033
  [1] healthy healthy healthy healthy healthy healthy healthy healthy healthy
 [10] healthy healthy healthy healthy healthy healthy healthy healthy healthy
 [19] healthy healthy healthy healthy healthy healthy healthy healthy healthy
 [28] healthy healthy healthy healthy healthy healthy healthy healthy healthy
 [37] healthy healthy healthy healthy healthy healthy healthy healthy healthy
 [46] healthy healthy healthy healthy healthy cancer  cancer  cancer  cancer 
 [55] cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer 
 [64] cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer 
 [73] cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer 
 [82] cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer 
 [91] cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer  cancer 
[100] cancer  cancer  cancer 
Levels: cancer healthy

sda documentation built on Nov. 22, 2021, 1:07 a.m.