GSVA from DESeq2

Question

[herny.bahus]

Hi, I'm analyzing RNA-seq data and i followed DESeq2 tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-un-normalized-counts) starting from the raw counts for gene expression, I want now to perform GSVA analysis with gsva() and i have a doubt on which assay to use, It's better to use the normalized data from the DESeq object or the assay output from vst()?

[igor]

The developer has previously addressed this question on the Bioconductor Support Site:

• https://support.bioconductor.org/p/107466/
• https://support.bioconductor.org/p/9141192/