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Change order of log transformation and normalisation in standard workflow #547

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merged 2 commits into from
Dec 2, 2024
Merged

Change order of log transformation and normalisation in standard workflow #547

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1a9df9f
Change order of log transformation and normalisation in standard work…
henninggaertner Nov 20, 2024
17f3c9c
Fix test for new order of steps
henninggaertner Nov 20, 2024
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4 changes: 2 additions & 2 deletions tests/protzilla/test_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,8 @@ def test_runner_imports(
'FilterSamplesByProteinIntensitiesSum',
'ImputationByKNN',
'OutlierDetectionByLocalOutlierFactor',
'NormalisationByMedian',
'TransformationLog',
'NormalisationByMedian',
'PlotProtQuant',
'DifferentialExpressionTTest',
'PlotVolcano',
Expand All @@ -109,8 +109,8 @@ def test_runner_imports(
call({'deviation_threshold': 2.0}),
call({'number_of_neighbours': 5}),
call({'number_of_neighbors': 20}),
call({'percentile': 0.5}),
call({'log_base': 'log2'}),
call({'percentile': 0.5}),
call({'similarity_measure': 'euclidean distance'}),
call({'alpha': 0.05}),
call({'fc_threshold': 1}),
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14 changes: 7 additions & 7 deletions user_data/workflows/standard.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,20 +36,20 @@ steps:
plot_inputs: { }
type: OutlierDetectionByLocalOutlierFactor
- form_inputs:
percentile: 0.5
log_base: log2
inputs: { }
plot_inputs:
graph_type: Boxplot
graph_type: Histogram
group_by: None
visual_transformation: log10
type: NormalisationByMedian
type: TransformationLog
- form_inputs:
log_base: log2
percentile: 0.5
inputs: { }
plot_inputs:
graph_type: Histogram
graph_type: Boxplot
group_by: None
type: TransformationLog
visual_transformation: log10
type: NormalisationByMedian
- form_inputs:
similarity_measure: euclidean distance
inputs: { }
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