Hi all, I have an RNAseq data for 81 samples. I ran ssGSEA 2.0 (I cloned it from the Broad Institute's github repository and sourced the code through R). After running the analysis a first time, I was curious whether somehow the score generated for any given sample was affected by other samples present. I re-ran the analysis using half of the samples, and to my surprise obtained slightly different results. However, upon repeating the analysis with the exact same parameters, again different results were obtained.
I conclude that the algorithm is somehow stochastic, explaining different results even despite identical input parameters. However, I still do not know whether the presence of other samples influences the output. Would anyone be able to enlighten me?
Thanks in advance.