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Based on the current formulation of the FDR, datasets having high decoy scores can lead to FDR values > 1 leading to loss of some annotations when preparing results by applying a cutoff of FDR < 1 (https://github.com/metaspace2020/metaspace/blob/6661211be8c87c2ff617f2cb8716a128bdc3915d/metaspace/engine/sm/engine/annotation_lithops/prepare_results.py#L74). This fixes the FDR calculation by adding the weighted decoy term to the denominator as well to make sure that FDR is always [0-1].
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Based on the current formulation of the FDR, datasets having high decoy scores can lead to FDR values > 1 leading to loss of some annotations when preparing results by applying a cutoff of FDR < 1 (
metaspace/metaspace/engine/sm/engine/annotation_lithops/prepare_results.py
Line 74 in 6661211
This fixes the FDR calculation by adding the weighted decoy term to the denominator as well to make sure that FDR is always [0-1].