arabid: Subset of Arabidopsis RNA-Seq Data

Description

A subset of RNA-Seq data studying the defense response of Arabidopsis thaliana to a bacterial infection. Two treatment groups were analyzed in the study: a mock inoculation ("mock") and a bacteria ("hrcc"). Three independent samples were used for each treatment. The 200 genes in this subset were randomly selected without replacement from the 26,222 genes in the original dataset. The rows in this matrix correspond to genes and the columns correspond to samples. Each individual cell of the matrix contains the counts of the RNA-Seq reads that are mapped to a reference database of known genes.

Usage

data(arabid)

Arguments

Format

A 200 by 6 matrix of RNA-Seq read frequencies.

Source

Di, Y., Schafer, D. W., Cumbie, J. S., & Chang, J. H. (2011). The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Statistical Applications in Genetics and Molecular Biology, 10, 1-28.

Examples

Run this code

	
	## These examples may each take a few minutes to compute
	
	## Obtain Dataset
	data(arabid)
			
	## Analysis of Count Data using Internal and Stability Validation Measures
	count1 <- optCluster(arabid, 2:4, clMethods = "all", countData = TRUE)
	topMethod(count1)
	
	## Analysis of Normalized Data using Internal and Stability Validation Measures
	obj <- t(t(arabid)/colSums(arabid)) ## Normalized with Respect to Library Size
	norm1 <- optCluster(obj, 2:4, clMethods = "all")
	topMethod(norm1)

Run the code above in your browser using DataCamp Workspace