DESeq (version 1.24.0)

plotPCA: Sample PCA plot from variance-stabilized data

Description

This plot helps to check for batch effects and the like.

Usage

plotPCA(x, intgroup = "condition", ntop = 500)

Arguments

x

an ExpressionSet, as obtained from varianceStabilizingTransformation

intgroup

ntop

how many of the most variable genes should be used in calculating the PCA

Value

a plot is produced

See Also

varianceStabilizingTransformation

Examples

cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
cds <- estimateDispersions( cds, method="blind" )
vsd <- varianceStabilizingTransformation( cds )
plotPCA( vsd )