I have a single RNA-Seq sample analyzed with kallisto and the output is a tsp with 170k lines (transcripts) and tpm values. I want to do single sample pathway enrichment (gene set enrichment), but I am not sure what, how to further preprocess the Kallisto output to fit into gsva, esp.:
1.) I need Entrez gene ids as input, I guess. However, I have multiple transcripts of a gene in Kallisto output. Is this a problem? 2.) Do I need any z-transformation?
Thank you very much for your help,