plotPCA {DESeq} | R Documentation |
This plot helps to check for batch effects and the like.
plotPCA(x, intgroup = "condition", ntop = 500)
x |
an ExpressionSet, as obtained from |
intgroup |
|
ntop |
how many of the most variable genes should be used in calculating the PCA |
a plot is produced
Wolfgang Huber
varianceStabilizingTransformation
cds <- makeExampleCountDataSet() cds <- estimateSizeFactors( cds ) cds <- estimateDispersions( cds, method="blind" ) vsd <- varianceStabilizingTransformation( cds ) plotPCA( vsd )