Question about GSVA

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 .

Start with the linked GSVA vignette and the refine.bio example that supplies the expression data; no repository file or test is named in the issue. Compare the documented input-normalization approaches and determine whether the example or its explanation needs clarification. Done means providing a supported answer and updating the relevant tutorial material if the interpretation is misleading.

Written by the indexing model from the issue text.