ssGSEA reports only one gene list
I have been running GSEA successfully with my gct file containing normalized reads from DeSeq2. But when I run the same gct file in ssGSEA with, for example, the HALLMARK collection, the output is only one of the 50 gene sets. Same thing happens with other gene set collections. What do I need to do different to get results on all the gene sets in a collection?
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