nki-ccb/transact_manuscript

Scripts supporting TRANSACT manuscript

transact_manuscript's Issues

where is file "read_GDSC "?

Thanks for your work!. When I run GSDC cross validation module, there was an error:

Traceback (most recent call last):
  File "GDSC_TCGA_cross_validation_with_combat.py", line 65, in <module>
    from read_GDSC import read_GDSC_drug_response
ModuleNotFoundError: No module named 'read_GDSC'

I cannot find any file named "read_GDSC" in your project. It seems you uploaded an earlier version of deep learning cv fold. Could you please update your code to make it work?

wget url to supplementary data seems not up to date

Hello, thank you very much for your work,

In the download_TCGA script, an error occurs after running the wget command

ERROR 403: Forbidden

It seems the URL to the supplemental data is not up to date.

figure_1.ipynb

Since I am not familiar with python, we started running from the example function (data_df = read_data) and got the following error:
`TypeError Traceback (most recent call last)
in
----> 1 data_df = read_data(tissues=tissues,
2 data_types=[e for e in data_types],
3 projects=projects,
4 data_sources=data_sources,
5 folder_basis='../data/')

F:\TRANSACT\read_data\read_data.py in read_data(tissues, data_types, projects, data_sources, folder_basis)
79 folders[s] = folder_basis + s
80
---> 81 data_df = {
82 s: upload_methods[s](data_types=data_types,
83 tissues=tissues[s],

F:\TRANSACT\read_data\read_data.py in (.0)
80
81 data_df = {
---> 82 s: upload_methods[s](data_types=data_types,
83 tissues=tissues[s],
84 projects=projects[s],

F:\TRANSACT\read_data\read_TCGA_data.py in read_TCGA_data(data_types, tissues, projects, folder)
60 # Merge samples since correlations are very good
61 data_df[i] = data_df[i].reset_index().groupby('index').agg('mean')
---> 62 unique_samples = reduce(np.intersect1d, [data_df[i].index for i in data_df])
63
64 return {d:data_df[d].loc[unique_samples] for d in data_df}

TypeError: reduce() of empty sequence with no initial value
`
In addition, we do not have a good understanding of the functions provided by TRANSACT (file:///C:/Users/Asus/anaconda3/pkgs/TRANSACT-main/html/transact/TRANSACT.html#references). A full running display may be valid.
Thank you very much for your attention and consideration.