PCA with DESeq2 Data

Question

[pthom010]

I conducted an RNAseq analysis with DESeqq2 and have a VST-transformed data frame I saved. I would like to do a PCA analysis with certain samples. Would anybody know if this is feasible?

Answer 1

[Trivas]

The DESeq2 vignette is pretty helpful with this. http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#principal-component-plot-of-the-samples. Their vsd is a vst transformed dds and so should translate really easily to your data.