VST in DESeq2 giving negative values

Question

[sanatbhadsavle]

Hi, I used the varianceStabilizingTransformation function on my dds object. However, the VST output results in negative values for certain genes, is that supposed to happen? I know this can happen with the rlog transformation, but does it also happen with vst ?

Answer 1

[ATpoint]

https://support.bioconductor.org/p/85983/#85985