What are ntop on plotPCA vsd in DESeq2?

Question

[ecg1g15]

I am trying to understand the following DESeq PCA code:

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

VERY different to the differentially expressed subset of genes from here:

de <- rownames(res[res$padj<0.05 & !is.na(res$padj), ]) 

plotPCA(vsd[de,], intgroup = "condition", ntop = 500)

What are thos ntop=500 selected at the beginning then? based on what are they TOP?

[Kevin Blighe]

C: DESeq2: subset dds or vsd to plot PCA with specific genes only

Answer 1

[ATpoint]

Please read the help ?DESeq2::plotPCA

ntop: number of top genes to use for principal components, selected by highest row variance