Questions Regarding the Execution of CausalPath

[abull271]

Hello, I would like to ask for advice on how to adjust my parameters when this error occurs. I have set the value to SignedP and also added the parameter value-transformation = signed-p-values, but it still fails to detect upregulation and downregulation. I cannot find a solution.
Exception in thread "main" java.lang.RuntimeException: Unknown parameter: change-detector
at org.panda.causalpath.run.CausalPath.setParameter(CausalPath.java:340)
at org.panda.causalpath.run.CausalPath.lambda$readParameters$3(CausalPath.java:333)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
at java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
at java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.util.Iterator.forEachRemaining(Unknown Source)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
at java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source)
at java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.util.stream.ReferencePipeline.forEach(Unknown Source)
at org.panda.causalpath.run.CausalPath.readParameters(CausalPath.java:333)
at org.panda.causalpath.run.CausalPath.(CausalPath.java:325)
at org.panda.causalpath.run.CausalPath.main(CausalPath.java:317)

[ozgunbabur]

Hi, did you put a parameter named "change-detector" in your parameters file? There is no such parameter defined in the guidelines.

[abull271]

No, I haven't used this parameter. Additionally, I found that my CausalPath can generate Protein results for lung adenocarcinoma, but fails to produce PTM data for the same cancer type. Conversely, it can yield PTM data for lung squamous cell carcinoma yet cannot generate Protein data for this cancer type—despite both datasets sharing the same format

[ozgunbabur]

Interesting. Is it possible to share your parameters file and the data file (can be partial) here? I can try running it in debug mode and see what is happening.

[abull271]

LUAD_Protein_CausalPath.txt

LUAD_PTM_CausalPath.txt

LSCC_PTM_CausalPath.txt

LSCC_Protein_CausalPath.txt

parameters.txt

[ozgunbabur]

Thanks for the files. Here are the issues I see.

1. You used the Symbols column for alternative symbols of the same gene. This is a misuse. Please only include the official HGNC symbol here and don't add another symbol unless that row corresponds to two different gene symbols.

2. In the PTM files, when there are multiple symbols in the Symbols column, the Sites column must have the same number of sites separated with a space, indicating the site number on each protein in the same order. But in your case I think you didn't mean to include multiple genes per row, so when you fix the previous issue, this will not be a problem anymore.

3. If you want to analyze Protein and PTM together (why not), you can simply combine these files, add a new Column named "Feature", and indicate what kind of measurement each row is. In that column, "G" means global proteomic measurement (for the rows coming from "Protein" files), and "P" is for a phosphoproteomic row (coming from your PTM files). If you do that, you also need to update the parameters.txt file to include the following.

feature-column = Feature
threshold-for-data-significance = 0.1 protein
threshold-for-data-significance = 0.1 phosphoprotein

Please also see the feature-column parameter definition here.

Please let me know if something is not clear. Happy to help further if you still get problems.

[abull271]

Thank you very much for your insightful reply. This has been the most helpful guidance I have received in recent days. Please accept my sincere wishes.