Preparation of a matrix of expression values of RNA-seq for input data of ssGSEA

Question

[Apprentice]

Hi.

I would like to do ssGSEA2.0 (https://github.com/broadinstitute/ssGSEA2.0) using my expression data of RNA-seq. About the input data of ssGSEA2.0, I have some questions.

1. My RNA-seq expression data is a matrix of FPKM values processed by StringTie. ssGSEA can I use the values of this matrix as input data? Can I just use the matrix values as input to ssGSEA or do I need to do a log2 transformation?

2. When performing differential expression analysis or general GSEA (not ssGSEA) using gene expression data, to reduce the number of false positives, genes with low mean values of expression level or low variance value of expression levels should be excluded in advance as input data. Should I use the input data of ssGSEA as input data after these processes? Or is it better to use the data without any processing as input data?

I would be grateful for your advice.