plotPCA {DESeq} | R Documentation

## 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

### Author(s)

Wolfgang Huber

### See Also

`varianceStabilizingTransformation`

### Examples

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

[Package DESeq version 1.39.0 Index]