## #1792 closed defect (fixed)

# Incorrect average method specified in IntensityTransform

Reported by: | Nicklas Nordborg | Owned by: | everyone |
---|---|---|---|

Priority: | critical | Milestone: | BASE 3.2.4 |

Component: | core | Version: | |

Keywords: | Cc: |

### Description (last modified by )

The possibility to store log-transformed data values in BASE was introduced a long time by #1120 (BASE 2.12). The information is stored as a "flag" (=`IntensityTransform`

) on the `BioAssaySet`

level.

Since the transformation changes the rules how averages (over the spot intensities) are calculated the `IntensityTransform`

flag was linked with the average method to use (a `Formula.AverageMethod`

object).

The problem is that incorrect average method was selected. The correct should be:

- NONE: Geometric
- LOG2: Arithmetic
- LOG10: Arithmetic

### Change History (3)

### comment:1 Changed 9 years ago by

Resolution: | → fixed |
---|---|

Status: | new → closed |

### comment:2 Changed 9 years ago by

Description: | modified (diff) |
---|

### comment:3 Changed 9 years ago by

(In [6365]) References #1792: Normalizers should store data in the same transform as the source data

Fixed for the `MedianRationNormalization`

plug-in. For 1-channel data, we use whatever that is stored in the database so we don't have to un-log and log data if the source is log-transformed.

For 2-channel data, log-transformed source data is first untransformed and then log-transformed again at the end.

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(In [6364]) Fixes #1792: Incorrect average method specified in IntensityTransform?