ex1620 {Sleuth3}

Differential Gene Expression with RNA Sequencing

Description

In an experiment to identify genes of the plant Arabidopsis that react to a particular pathogen, researchers used RNA sequencing to produce gene profiles for a number of plants not subjected to the pathogen and several plants subjected to the pathogen. Tests comparing the distribution of gene expression in the two groups were performed for each gene individually. The data are the p-values from all these tests. The goal is to use a identify a set of genes that differentially express in the two groups, subject to some specified value for expected false discovery rate, such as 5%.

Usage

ex1620

Format

A data frame with 20,245 observations on the following 3 variables.

Gene

an identification number for genes

GeneName

a character variable with the name of the gene

pValue

the p-value from a test that the mean expression level for the gene differs in the two groups (ignoring multiple testing)

Source

Ramsey, F.L. and Schafer, D.W. (2013). The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed), Cengage Learning.

References

Chang, J, Department of Botany and Plant Pathology, Oregon State University, personnal communication.

Examples

str(ex1620)