Good evening.
While using R, the output of ssGSEA is given in graphs for each rank plot (pdf), signatures_gct, final_ssGSEA-combined.gct, final_ssGSEA-fdr-pvalues.gct, final_ssGSEA-pvalues/gct and final_ssGSEA-scores.gct (example given in the mail). However, if I try to represent the.gct files, this using the heatmap of GenePattern, an error is generated.
While using GenePattern, the output of ssGSEA is the enriched scores.gct. When I perform the heatmap using GenePattern, it is easily generated.
What is the difference between the output of ssGSEA using R and Gene Pattern? How do I proceed with the output of R that I have after performing ssGSEA?
Thanking you.
Like it is mentioned in the ssGSEA website (https://gsea-msigdb.github.io/ssGSEA-gpmodule/v10/index.html) the output GCT file from Genepattern ssGSEA can serve as input into GenePattern’s other clustering and classification algorithms.
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