ssGSEA ROC module error message

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Mario Ezquerra

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Oct 25, 2022, 5:15:54 AM10/25/22
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Hi, I launched the ROC curve module and the software gives me this message error. I think that the CLS and GCT files are correct, so I am not sure about the origin of problem, any idea?

Thanks

Mario



Warning message: In readLines(clsfile) : incomplete final line found on '/opt/gpcloud/gp_home/users/Marioezq/uploads/tmp/run1804698797315094022.tmp/CLS/2/Train name CLS_PD.cls' Error in prediction(as.numeric(eval(parse(text = paste0("dataset$", dataset_calculations[dataset_calculations[c(1)] == : Number of predictions in each run must be equal to the number of labels for each run. Execution halted
data_test PD.gct
name CLS_PD.cls

Anthony Castanza

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Oct 25, 2022, 1:21:08 PM10/25/22
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Hi Mario,

It appears that this error is resulting from some extreme behavior in the calculation of the Matthews correlation coefficient matrix for the null permutations resulting in NAN computations. I'll have to dig deeper into this error, but it would appear that I missed an edge-case when writing this module.
Hopefully I can resolve this and get a fix out but I can't really offer much of an ETA there, sorry!

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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Anthony Castanza

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Oct 25, 2022, 2:12:41 PM10/25/22
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Hi Mario,

Quick follow up. I have a workaround for you. If you change the names of your gene sets to replace the "-" with "_" the calculations will go through. There is an issue in R where the "-" character gets replaced in column names and this messes up the matching that we're doing in the ssGSEA_ROC script. I've attached a fixed GCT that should run here.

Let me know if you have any questions, or if this fix doesn't work for you

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
data_test PD.gct
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