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PathwayAndDataAnalysis / causalpath

A project for exploring differentially active signaling paths related to proteomics datasets
GNU Lesser General Public License v3.0
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getChangeSign can be called only after setting the change detector #28

Open DahhamAlsoud opened 6 days ago

DahhamAlsoud commented 6 days ago

Hi! Thanks for making this nice tool available!

I'm trying to use CausalPath for RNAseq data using these parameters: proteomics-values-file = xxx.txt id-column = ID symbols-column = Symbols sites-column = Sites effect-column = Effect value-transformation = signed-p-values value-column = Value threshold-for-data-significance = 0.05 rna calculate-network-significance = true permutations-for-significance = 10000 fdr-threshold-for-network-significance = 0.05 use-network-significance-for-causal-reasoning = true minimum-potential-targets-to-consider-for-downstream-significance = 10 color-saturation-value = 10 show-all-genes-with-proteomic-data = false data-type-for-expressional-targets = rna use-expression-for-activity-evidence = true

I left sites and effects empty

I receive this error: Exception in thread "main" java.lang.RuntimeException: getChangeSign can be called only after setting the change detector. at org.panda.causalpath.data.ExperimentData.getChangeSign(ExperimentData.java:60) at org.panda.causalpath.analyzer.DataLabelShuffler.convert(DataLabelShuffler.java:134) at org.panda.causalpath.analyzer.DataLabelShuffler.convert(DataLabelShuffler.java:118) at org.panda.causalpath.analyzer.DataLabelShuffler.init(DataLabelShuffler.java:52) at org.panda.causalpath.analyzer.DataLabelShuffler.(DataLabelShuffler.java:33) at org.panda.causalpath.analyzer.NSCForComparison.run(NSCForComparison.java:60) at org.panda.causalpath.run.CausalPath.calculateNetworkSignificance(CausalPath.java:777) at org.panda.causalpath.run.CausalPath.run(CausalPath.java:586) at org.panda.causalpath.run.CausalPath.main(CausalPath.java:317)

It seems that a "chDet" object should be initialized/assigned, but I couldn't find any further solution..

Any further guidance would be appreciated!

Thank you Dahham

ozgunbabur commented 5 days ago

Hi Dahham,

The problem is that the software does not understand your data is RNAseq. There is a mechanism to designate the kind of omics of each data row. Add a "Feature" column to your data file and make it display "R" (without quotes, meaning the row is RNA measure) on each row. Then add the parameter "feature-column = Feature" in the parameters.txt file.

Let me know if this resolves the issue.

Ozgun

DahhamAlsoud commented 4 days ago

Hi Ozgun,

Thank you very much for your prompt and kind answer!

Adding the "Feature" column as you described indeed resolved my issue!

Thank you very much! Dahham