ssGSEA for beginners
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5 months ago
mk.gill • 0

Dear ssGSEA users, I am a biologist trying to do RNA-seq analysis for breast cancer PanCancer Atlas dataset obtained from cbioportal. I have generated gene expression input file (.gct) and geneset (.gmt) file and ran ssGSEA using the module on the GenePattern platform with default parameters. As a test run, I prepared a gene expression input file(.gct) for 1 sample and 20502 genes (rows). I am trying to understand output file gct-scores.txt
1.What does the column "signature.set.overlap.sample ID" represent? My geneset file list 55 genes. Twenty-five genes appeared in the column "signature.set.overlap.sample ID". 2.Got score 9.66. What does this score mean? How to interpret this score? What is the significant score range?

Thank you. Best, Mandeep

rna-seq ssGSEA R Gene Pattern • 289 views

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