Hi,

I am using DESeq2 1.18 and had some problem with getVarianceStabilizedData.

The CountDataSet was produced internally 

>cds <- homemade.CountDataSet(project, "gene", feature.ids = "count")

I can check its class:

> class(cds)

[1] "CountDataSet"

attr(,"package")

[1] "DESeq"

It is fine be to used in the following code:
>dds <- DESeqDataSetFromMatrix(countData = counts(cds),
                              colData = ph,
                              design= ~ SAMID)
>dds <- DESeq(dds)

but when I tried to:
>vsdMat <- getVarianceStabilizedData(dds)

an error msg was throw out:

Error: is(cds, "CountDataSet") is not TRUE

It does not make sense since :

> is(cds, "CountDataSet")

[1] TRUE

I tried to search here but it seems be to an old bug in older version of DESeq. But I am using a relative new version. 

thanks and best,

Lily 

DESeq2 has its own functions and classes. It looks like you’re trying to mix DESeq the old version with DESeq2. Id recommend to just follow the DESeq2 vignette or workflow.