Array Index Error

[vamikakarn]

Hi
I am trying to run CausalPath on cptac phosphoproteomics data, however I keep getting this error:

directory = C:\Users\user\Desktop\causalpath\trial
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 171
at org.panda.causalpath.resource.ProteomicsFileReader.readAnnotation(ProteomicsFileReader.java:62)
at org.panda.causalpath.run.CausalPath.run(CausalPath.java:385)
at org.panda.causalpath.run.CausalPath.main(CausalPath.java:317)

[ozgunbabur]

Can I see your input files please? You may have misspelled the name of the ID column in the parameters file.

[vamikakarn]

parameters.txt
phosphoproteomics.txt

Here are my input files.

[ozgunbabur]

CausalPath requires that the dataset has an ID for each row. This is missing in your files. You can insert a new column named "ID", and fill it with the combination of the symbol and the site, such as NRF1_S136. Just make sure that IDs are unique.

After this change, you also need to specify the ID column in the parameters file by adding "id-column = ID"

Let me know if this resolves your issue.

[vamikakarn]

Tried it. Getting the error:
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 170 out of bounds for length 170
at org.panda.causalpath.resource.ProteomicsFileReader.readVals(ProteomicsFileReader.java:143)
at org.panda.causalpath.resource.ProteomicsFileReader.addValues(ProteomicsFileReader.java:172)
at org.panda.causalpath.run.CausalPath.run(CausalPath.java:390)
at org.panda.causalpath.run.CausalPath.main(CausalPath.java:317)

[ozgunbabur]

Can you upload the modified files?

[vamikakarn]

cptac-data.zip

[ozgunbabur]

That was due to a bug in handling missing values. I fixed it in the code, but it will take a while to put it in the release.

How do you run CausalPath? If you are running it from the sources, following the instructions on the GitHub front page (https://github.com/PathwayAndDataAnalysis/causalpath), then please update the project (git pull) and try again.