I am using the DESeq package to do a DE analysis. I would like to plot the PCA plot and Dispersion estimates plot in r studio. However, I am running into errors.

I tried to construct an DESeq specific object called CountDataSet to hold count and pheno data:

y.DESeq<-newCountDataSet(countdata1, finaldata1$Group) 

y.DESeq.norm <- estimateSizeFactors(y.DESeq)

y.DESeq.norm2<- estimateDispersions(y.DESeq.norm, method="blind")

vsd <- varianceStabilizingTransformation(y.DESeq.norm2)

I got errors like "unable to find an inherited method for function ‘normalizationFactors’ for signature ‘"CountDataSet"’, and the same for plotDispEsts(y.DESeq.norm).

Does anyone know the reason and how do I fix that?

Thanks in advance