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Multiple identifiers mapped to a single gene in "Remap_Only" mode

GSEA's "Remap_Only" collapsing mode is designed to convert gene identifiers across transcriptome versions, but does not perform any mathematical operations to handle multiple input symbols mapping to the same output symbol. The GSEA application only supports single instances of a given gene symbol in an analysis run. When GSEA encounters the case of multiple instances of the same gene symbol, the first instance is retained and the later instances are arbitrarily discarded. In order to prevent producing this arbitrary output, when multiple input values mapping to a single output value are encountered in Remap_Only mode, the attempt to remap symbols fails and returns Error 1020.

In order to remedy this error, it is recommended to choose an appropriate mathematical collapse function for the input data set, whereby multiple identifiers corresponding to the same gene will be collapsed to a single entry in the output file.
GSEA supports the following options for performing this mathematical collapse:

  • Max_probe
  • Median_of_probes
  • Mean_of_probes
  • Sum_of_probes
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