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Add a secondBaselineGroup field to DifferentialExpressionAnalysisResultSet and backfill baselines for interactions #1122

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arteymix opened this issue May 9, 2024 · 2 comments · May be fixed by #1139
Open
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Add a secondBaselineGroup field to DifferentialExpressionAnalysisResultSet and backfill baselines for interactions #1122

arteymix opened this issue May 9, 2024 · 2 comments · May be fixed by #1139
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1.32.0

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arteymix commented May 9, 2024 •
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In c2f4dfc, we're computing the baselines for interaction terms on-the-fly. This is not ideal as it can be done when the result set is created.

  •  add a secondBaselineGroup field to DifferentialExpressionAnalysisResultSet
  • populate it when we perform the linear model
  • backfill values using baselines of individual factors

I'm not sure we allow interaction of continuous factors, but in that case those inherently lack a baseline.

There might be a case when a continuous factor interacts with a categorical one, in which case we should also fill one of the baselines. @ppavlidis is this possible?
@arteymix arteymix added this to the 1.32.0 milestone May 9, 2024
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arteymix commented May 9, 2024

One added benefit to this is that those result sets will become discoverable. In the REST API, we should plan for a pseudo-property that maps to either first or second baseline group (i.e. a baselineGroups collection).

@arteymix arteymix linked a pull request Jun 6, 2024 that will close this issue
Add a second baseline group and a migration to port existing result sets #1139
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@arteymix arteymix mentioned this issue Jun 26, 2024
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@arteymix arteymix modified the milestones: 1.32.0, 1.31.9 Jun 26, 2024
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arteymix commented Jun 26, 2024 •
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This would be helpful to resolve two issues: #975 and #1164. The alternative is to reuse the logic for computing baselines on-the-fly, but that might be prohibitive in the case of getting all DE results for a given gene.

@arteymix arteymix modified the milestones: 1.31.9, 1.31.10, 1.32.0 Jul 29, 2024
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Add a second baseline group and a migration to port existing result sets PavlidisLab/Gemma
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