ssGSEA normalization method selection

[Maite E]

Hi,

I am performing a ssGSEA in GenePattern. My input data is TPMs. I am unsure about what normalization method to select among "none", "rank", "log", "log.rank". I read the documentation, and it says the following:

• Sample normalization method*
  • Normalization method applied to expression data (if the option “none” is selected, data will not be normalized). Supported methods are none, rank, log.rank, and log. (Default: none)

It is not clear to me whether I should select the normalization method I already applied, or the one GenePattern will apply when calculating my ssGSEA values. If the second option, what normalization method do you recommend to apply and why?

Thank you!

Maite