Opened 10 years ago

Closed 10 years ago

## #273 closed defect (fixed)

# Bug in detection p-value

Reported by: | Jari Häkkinen | Owned by: | Jari Häkkinen |
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Priority: | major | Milestone: | Illumina package v1.5.1 |

Component: | net.sf.basedb.illumina | Keywords: | |

Cc: |

### Description

This bug affects all previous versions of the detection p-value plug-in. The error is small and has minor impact on calculated p-values.

The MAD outlier part of the algorithm sometimes excludes small intensity negative control probes from the detection p-value calculation. This case was not considered prior to this fix. This omission decreased the p-value with a small number and consequently the smallest p-value could become less than zero and p-value 1 could not be reached.

The resolution of this ticket solved the above problem and changes the border for zero p-value such that no probe with intensity equal or less than the largest negative control can achieve a zero p-value. Note, there may be negative control probes with larger intensities than the ones used in the detection p-value calculation (MAD outliers).

### Change History (3)

### comment:1 Changed 10 years ago by

Status: | new → assigned |
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### comment:2 Changed 10 years ago by

Type: | Request → defect |
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### comment:3 Changed 10 years ago by

Resolution: | → fixed |
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Status: | assigned → closed |

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(In [1232]) Fixes #273