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Correct GSEA mislabeling in g:Profiler (web) chapter - #33

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hosseinvk/fix-gprofiler-gsea-mislabel
Aug 10, 2026
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Correct GSEA mislabeling in g:Profiler (web) chapter#33
hosseinvk merged 1 commit into
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hosseinvk/fix-gprofiler-gsea-mislabel

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Summary

  • g:Profiler's "Ordered query" mode is incremental ORA over prefixes of a ranked list, not the Subramanian et al. 2005 GSEA algorithm (no running-sum statistic, no ranking-metric-magnitude weighting, no permutation testing).
  • Retitled "Steps to perform GSEA-style analysis in g:Profiler" -> "Steps to use a ranked gene list in g:Profiler", and the challenge "GSEA with gProfiler" -> "Ranked-list ORA with gProfiler".
  • Added a short note explicitly contrasting the two methods, since this chapter now sits right after the real GSEA (web) chapter in the book.
  • Corrected the intro line's claim that gProfiler "supports both ORA and GSEA".

Test plan

  • Full bookdown::render_book() completes cleanly.
  • Confirmed the cross-reference link target (gsea-web.html) matches the chapter's actual rendered slug.
  • CI bookdown-render job to be confirmed green before merge.

g:Profiler's "Ordered query" mode runs incremental ORA (hypergeometric
test) over prefixes of a ranked list; it does not implement the
Subramanian et al. 2005 GSEA algorithm (no running-sum statistic, no
weighting by ranking-metric magnitude, no permutation testing). This
was previously labelled "GSEA-style analysis" and "GSEA with
gProfiler", which risks confusing readers now that this chapter sits
right after the real GSEA(web) chapter. Retitled the section and
challenge, added a clarifying note contrasting the two methods, and
corrected the intro line's claim that gProfiler "supports both ORA
and GSEA".
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hosseinvk merged commit 2b50957 into main Aug 10, 2026
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hosseinvk deleted the hosseinvk/fix-gprofiler-gsea-mislabel branch August 10, 2026 00:56
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