Question about GSVA

[dvenprasad]

Came in via refine.bio examples feedback form.

Appreciate the tutorial, however I was wondering if the GSVA input from RNA-Seq expression data should be normalized within each sample using methods such as RSEM TPM instead of the between sample variance stabilized method using DESeq2. The GSVA vignette written by the authors (https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.html#5_Quantification_of_pathway_activity_in_bulk_microarray_and_RNA-seq_data
) used log(CPM) from edgeR which I believe is more similar to TPM and RPKM than vst counts.

Please let me know if I made a mistake in my interpretation and hope this message can help both of us! Thank you in advance!

We can reach out to them if need to ask questions/ and respond to them .