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GSEA attempted to collapse each probe set in the dataset to a gene, but there was no data in the resulting dataset. The most likely reasons for this are

  • You are attempting to collapse a dataset that is already collapsed.
  • The probe identifiers in your dataset do not match the probe identifiers in the chip files selected in the chip platform(s) parameter.


Check the gene/probe identifiers in your dataset. If they are HUGO gene symbols, set the Collapse dataset to gene symbols parameter to False; the dataset is already collapsed. Otherwise, check that the probe identifiers in your dataset match the probe identifiers listed  in the chip file that you selected in the chip platform(s) parameter. For more information, see Consistent Feature Identifiers Across Data Files in the GSEA User Guide.

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