#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 by , 11 years ago
| Resolution: | → fixed |
|---|---|
| Status: | new → closed |
comment:2 by , 11 years ago
| Description: | modified (diff) |
|---|
comment:3 by , 11 years ago
(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.
(In [6364]) Fixes #1792: Incorrect average method specified in IntensityTransform