es: A Simulated Data Set

In countTransformers: Transform Counts in RNA-Seq Data Analysis

Description

A simulated data set based on the R code provided by Law et al.'s (2014) paper.

Usage

data("es")

Format

The format is: Formal class 'ExpressionSet' [package "Biobase"]

Details

The simulated data set contains RNA-seq counts of 1000 genes for 6 samples (3 cases and 3 controls). The library sizes of the 6 samples are not equal.

Source

The dataset was generated based on the R code Simulation_Full.R from the website http://bioinf.wehi.edu.au/voom/.

References

Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology. 2014; 15:R29

Examples

library(Biobase)

data(es)
print(es)

# expression set
ex = exprs(es)
print(dim(ex))
print(ex[1:3,1:2])

# phenotype data
pDat = pData(es)
print(dim(pDat))
print(pDat[1:2,])

# feature data
fDat = fData(es)
print(dim(fDat))
print(fDat[1:2,])

countTransformers documentation built on May 1, 2019, 7:59 p.m.