daisybio / daisybio/preprocess_drp_data
Normalization for CCLE
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Descrizione
I think the normalisation for CCLE is wrong.
Original code:
```{python}
# transfroms [0, -100] to [1,0] for curvecurator processing
def transform_activity_range(raw_df):
raw_df["Activity Data (median)"] = raw_df["Activity Data (median)"] / 100 + 1
raw_df["Amax"] = raw_df["Amax"] / 100 + 1
```
There is no explicit control column in the raw data, but there is this Amax value, which seems to be unique per cell line/drug combination. In the original supplementary methods, the authors state that
> Amax is the maximal activity value reached within a model
In the raw data, Amax is kind of the maximum response; it is always close to the response value associated with the highest dose (8µM). So it seems to be a positive control rather than a negative control, like DMSO would be.
I think it should be
```{python}
raw_df["response"] = 1 - raw_df["Activity Data (median)"]/raw_df["Amax"]
```
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Direzione di ricerca
Start by locating the CCLE preprocessing entry point and the transform_activity_range function, then inspect how "Activity Data (median)", "Amax", and response are used downstream. Done means the CCLE response normalization follows the stated positive-control interpretation of Amax and remains valid for the generated input files.
Scritto dal modello di indicizzazione a partire dal testo della issue.
Valutazione
- Stack tecnologico
- python
- Ambito
- data-engineering
- Tipo di issue
- Bug
- Difficoltà
- 3/5
- Tempo stimato
- 1-2 giorni
- Stato di attività
- Ferma
- Chiarezza
- Abbastanza chiara
- Idoneità per principianti
- 45/100