I'm using GSVA to get an overall activity/expression pattern of various gene sets using RNA-seq data. This is generally OK, but in my case, about half of the gene sets have only two genes, and I definitely don't want to discard them. As the GSVA help documentation recommends a minimum of 5 genes in the set, I was wondering if I'm getting useful/meaningful results at all for these very small gene sets. What do you think? If GSVA is not good in this case, are there any alternative methods that might be useful or should I just go with a summary of normalized TPM values for example?
Thanks for any suggestion!