Getting the normalized phospho-site data exported

[dorvashmr]

Hi,

Thank you for the amazing job your team did in developing this package (precisely because it is a python-based package ;-) ).

I had 3 questions:

1- As I realized, the "ProteomicsData" class gets the "phospho" data while the site position is there only as a single column. How would you set this DataFrame to include the site multiplicity?

2- Can I ask you to check my code and see if I'm using the package correctly?

### reading the phosphosite and protein files:
# Protein ID as the index:
protein = pd.read_table(total_proteomics_pg_matrix.tsv)
# Protein ID and site position as indices:
phospho = pd.read_table(phospho.tsv)


### column-normalizing the input files:
protein = phdc.column_normalize(protein, method='upper_quartile')
phospho = phdc.column_normalize(phospho, method='upper_quartile')

### making the ProteomicsData instance:
proteomics = phdc.ProteomicsData(phospho, protein)

### normalizing the phospho against proteins:
phospho_norm = proteomics.normalize_phospho_by_protein()

3- How can I get the "phospho_norm" DataFrame exported as a csv/tsv file? If that is possible, how can I get the values to be on the same scale as before the "column normalization" (input was log2-transformed values)?

Thank you very much again for your great work.

Cheers,
Reza