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
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 Jari Häkkinen

Status: newassigned

comment:2 Changed 10 years ago by Jari Häkkinen

Type: Requestdefect

comment:3 Changed 10 years ago by Jari Häkkinen

Resolution: fixed
Status: assignedclosed

(In [1232]) Fixes #273

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