daisybio / daisybio/preprocess_drp_data
Normalization for CCLE
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Description
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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