Original signal score file missing about lp-sda HOT 6 OPEN

Hi, I'm not able to find original signal score file in the repo.
When I created a folder named 'SignalScoresSource', I'm getting the following error:

Traceback (most recent call last):
File "run.py", line 115, in
more_main()
File "run.py", line 112, in more_main
main(args)
File "run.py", line 37, in main
data = FAERSdata(args.input, args.method, args.year)
File "/Users/user/Downloads/LP-SDA-master/FAERSdata.py", line 12, in init
Files = [Files[-1]]
IndexError: list index out of range

Please help.
Thanks in advance.

Hi,
as shown in line 9 of FAERSdata.py
Files = os.listdir('%s/%s' % (directory, method))
it will obtain the files under directory/method/. The "directory" name (bydefault) is "SignalScoresSource" and the "method" name is one of 'PRR05', 'ROR05', 'GPS', 'BCPNN'.
In order to run the code, your local input file structure should be

LP-SDA
│   run.py
│   ...  
└───SignalScoresSource
│   └───PRR05
│       │   prr_04.csv # for example, PRR signal scores using FAERS data collected until 2004
│       │   prr_05.csv
│       │   ...
│   └───ROR05
│       │   ror_04.csv 
│       │   ror_05.csv
│       │   ...
│   ...

The data structure for each signal score file is (demo)

| drug id | adr id | signal score
| 64564 | 2342 | 5.22

After having these computed signal score files, you should be able to run the experiments.

from lp-sda.

Hi, I'm not able to find original signal score file in the repo.
When I created a folder named 'SignalScoresSource', I'm getting the following error:
Traceback (most recent call last):
File "run.py", line 115, in
more_main()
File "run.py", line 112, in more_main
main(args)
File "run.py", line 37, in main
data = FAERSdata(args.input, args.method, args.year)
File "/Users/user/Downloads/LP-SDA-master/FAERSdata.py", line 12, in init
Files = [Files[-1]]
IndexError: list index out of range
Please help.
Thanks in advance.

Hi,
as shown in line 9 of FAERSdata.py
Files = os.listdir('%s/%s' % (directory, method))
it will obtain the files under directory/method/. The "directory" name (bydefault) is "SignalScoresSource" and the "method" name is one of 'PRR05', 'ROR05', 'GPS', 'BCPNN'.
In order to run the code, your local input file structure should be

LP-SDA
│   run.py
│   ...  
└───SignalScoresSource
│   └───PRR05
│       │   prr_04.csv # for example, PRR signal scores using FAERS data collected until 2004
│       │   prr_05.csv
│       │   ...
│   └───ROR05
│       │   ror_04.csv 
│       │   ror_05.csv
│       │   ...
│   ...

The data structure for each signal score file is (demo)

| drug id | adr id | signal score
| 64564 | 2342 | 5.22

After having these computed signal score files, you should be able to run the experiments.

Thanks for the reply.
Where can I find these PRR and ROR csvs?

from lp-sda.

Hi, I'm not able to find original signal score file in the repo.
When I created a folder named 'SignalScoresSource', I'm getting the following error:
Traceback (most recent call last):
File "run.py", line 115, in
more_main()
File "run.py", line 112, in more_main
main(args)
File "run.py", line 37, in main
data = FAERSdata(args.input, args.method, args.year)
File "/Users/user/Downloads/LP-SDA-master/FAERSdata.py", line 12, in init
Files = [Files[-1]]
IndexError: list index out of range
Please help.
Thanks in advance.

Hi,
as shown in line 9 of FAERSdata.py
Files = os.listdir('%s/%s' % (directory, method))
it will obtain the files under directory/method/. The "directory" name (bydefault) is "SignalScoresSource" and the "method" name is one of 'PRR05', 'ROR05', 'GPS', 'BCPNN'.
In order to run the code, your local input file structure should be

LP-SDA
│   run.py
│   ...  
└───SignalScoresSource
│   └───PRR05
│       │   prr_04.csv # for example, PRR signal scores using FAERS data collected until 2004
│       │   prr_05.csv
│       │   ...
│   └───ROR05
│       │   ror_04.csv 
│       │   ror_05.csv
│       │   ...
│   ...

The data structure for each signal score file is (demo)

| drug id | adr id | signal score
| 64564 | 2342 | 5.22

After having these computed signal score files, you should be able to run the experiments.

Thanks for the reply.
Where can I find these PRR and ROR csvs?

I didn't upload these original files. They can be easily computed using the existing R package (phvid) based on FAERS data.

from lp-sda.

phvid
Thanks for the reply :)

from lp-sda.

Hi, I'm not able to find original signal score file in the repo.
When I created a folder named 'SignalScoresSource', I'm getting the following error:
Traceback (most recent call last):
File "run.py", line 115, in
more_main()
File "run.py", line 112, in more_main
main(args)
File "run.py", line 37, in main
data = FAERSdata(args.input, args.method, args.year)
File "/Users/user/Downloads/LP-SDA-master/FAERSdata.py", line 12, in init
Files = [Files[-1]]
IndexError: list index out of range
Please help.
Thanks in advance.

Hi,
as shown in line 9 of FAERSdata.py
Files = os.listdir('%s/%s' % (directory, method))
it will obtain the files under directory/method/. The "directory" name (bydefault) is "SignalScoresSource" and the "method" name is one of 'PRR05', 'ROR05', 'GPS', 'BCPNN'.
In order to run the code, your local input file structure should be

LP-SDA
│   run.py
│   ...  
└───SignalScoresSource
│   └───PRR05
│       │   prr_04.csv # for example, PRR signal scores using FAERS data collected until 2004
│       │   prr_05.csv
│       │   ...
│   └───ROR05
│       │   ror_04.csv 
│       │   ror_05.csv
│       │   ...
│   ...

The data structure for each signal score file is (demo)

| drug id | adr id | signal score
| 64564 | 2342 | 5.22

After having these computed signal score files, you should be able to run the experiments.

Thanks for the reply.
Where can I find these PRR and ROR csvs?

I didn't upload these original files. They can be easily computed using the existing R package (phvid) based on FAERS data.

If possible can you please upload the csvs as well?

from lp-sda.

Hi, I'm not able to find original signal score file in the repo.
When I created a folder named 'SignalScoresSource', I'm getting the following error:
Traceback (most recent call last):
File "run.py", line 115, in
more_main()
File "run.py", line 112, in more_main
main(args)
File "run.py", line 37, in main
data = FAERSdata(args.input, args.method, args.year)
File "/Users/user/Downloads/LP-SDA-master/FAERSdata.py", line 12, in init
Files = [Files[-1]]
IndexError: list index out of range
Please help.
Thanks in advance.

Hi,
as shown in line 9 of FAERSdata.py
Files = os.listdir('%s/%s' % (directory, method))
it will obtain the files under directory/method/. The "directory" name (bydefault) is "SignalScoresSource" and the "method" name is one of 'PRR05', 'ROR05', 'GPS', 'BCPNN'.
In order to run the code, your local input file structure should be

LP-SDA
│   run.py
│   ...  
└───SignalScoresSource
│   └───PRR05
│       │   prr_04.csv # for example, PRR signal scores using FAERS data collected until 2004
│       │   prr_05.csv
│       │   ...
│   └───ROR05
│       │   ror_04.csv 
│       │   ror_05.csv
│       │   ...
│   ...

The data structure for each signal score file is (demo)

| drug id | adr id | signal score
| 64564 | 2342 | 5.22

After having these computed signal score files, you should be able to run the experiments.

Thanks for the reply.
Where can I find these PRR and ROR csvs?

I didn't upload these original files. They can be easily computed using the existing R package (phvid) based on FAERS data.

If possible can you please upload the csvs as well?

I uploaded one file under "SignalScoresSource/PRR05/prr05_14.csv", which is the signal scores computed by PRR using data up to 2014.

from lp-sda.