I am practicing DESeq2 manual (Differential analysi s of count data – the DESeq2 package). When I do
varianceStabilizingTransformation with dds created from my data I get "
Error: is(cds, "CountDataSet") is not TRUE". Surprisingly when I practiced the example from R's help page "Apply a variance stabilizing transformation (VST) to the count data", I got the same error again. Any suggestions? Please speak at non-bioinformatician level!
> dds <- makeExampleDESeqDataSet(m=6) > vsd <- varianceStabilizingTransformation(dds) Error: is(cds, "CountDataSet") is not TRUE