Alternatives to Gene Set Enrichment Analysis dedicated for single samples

Question

[orzech_mag]

Dear colleagues,

I would like to perform Gene Set Enrichment Analysis (or some alternative analysis) on the data that contain only two samples, which represent two phenotypes (one sample in one phenotype). I already performed regular GSEA with tTest and permutation regarding gene sets, however due to small size groups the results are insufficient. I would appreciate if you suggest me any other solution or alternative analysis or maybe some other settings of GSEA that considers such small groups as well. I do not mind R in case.

Thank you in advance!

Answer 1

[sysbiocoder]

There is an option in GSEA where you can rank genes based on fold change Check below post Input GSEA Pre-ranked list