I did my RNA-Seq analysis using the Galaxy platform with the following pipeline: HISAT2 --> featureCounts --> DESeq2.
Now I want to recreate the PCA plot in RStudio. In the DESeq2 manual, the command line for this is:
plotPCA(object, intgroup = "condition", ntop = 500, returnData = FALSE)
What is the format of the object/DESeqDataSet exactly?
Apologies for the basic question.