Question: Is the ssGSEA enrichment score affected by other samples in the analysis group?
gravatar for psm
15 days ago by
psm30 wrote:

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.

rna-seq R ssgsea • 102 views
ADD COMMENTlink modified 9 days ago by lixuenan20080630 • written 15 days ago by psm30

It is interesting.. I haven't never seen such a issue since I have run it. But you can also use the other packages for single sample analysis. I would recommend you to try GSVA and Singscore

ADD REPLYlink written 11 days ago by ugurcabuk110
gravatar for lixuenan200806
9 days ago by
lixuenan20080630 wrote:

I had met the same question, I run ssgsea2.0 with the same data and parameter two times, but i got the different score ,when i use median score as cutoff value,I got high low groups with different samples

ADD COMMENTlink modified 9 days ago • written 9 days ago by lixuenan20080630
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