Removal of discrete geeq fields and their replacements
@ppavlidis wanted to have the discrete geeq fields removed from the dataset endpoints. However the wrapper packages uses some components, so ideally they would be replaced. These fields are
- geeq.batchCorrected: boolean field. whether or not batch correction was performed on the dataset.
- geeq.batchConfound: 0 if no batch info, -1 if batch confound is detected, 1 if batch info is available and no batch confound detected
- geeq.batchEffect: -1 if p value <0.0001 1 if p value >0.1, 0 for everything else
I believe this information is sufficiently present in batchEffect enum and the newly populated batchEffectStatistics fields. though it's not particularly nice that batchEffectStatistics is free text.
- geeq.rawData, -1 if no raw data is available, 1 if raw data was available. This is only available by paying another visit to the quantitationTypes endpoing and looking at isRecomputedFromRawData
I can relocate some of these fields at the dataset level, where they belong.
The remaining fields can be moved to the admin GEEQ VO.
We could also simply expose the P-value of the batch effect although right now I think it's mangled in a string.
that'd actually be nice too