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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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Run_viper error #52

Closed Chengwei94 closed 2 years ago

Chengwei94 commented 2 years ago

This manage to run for run_wmean but run_viper encountered error

acts <- run_viper( mat = mat, network = net, .source = "source", .target = "target", .mor = "mor", minsize = 5, method = "scale", eset.filter = FALSE, cores = 1, verbose = T)

Computing the association scores Computing regulons enrichment with aREA |=======================================================================================================================| 100% Computing pleiotropy for 1497 samples.

Process started at Thu Apr 14 15:43:54 2022 | | 0%Error in if (tmp == 0) tmp <- 1 : missing value where TRUE/FALSE needed In addition: Warning message: In max(s1) : no non-missing arguments to max; returning -Inf`

PauBadiaM commented 2 years ago

Hi @Chengwei94 ,

Sorry but from this snipped of code and error message I cannot understand what might be wrong. Could you create a small reproducible example so that I can debug it? By the way, just in case try to run it without the argument method.

Chengwei94 commented 2 years ago

HI @PauBadiaM,

I think it might have been that some of my genes are all 0 that are causing the issue. After I filtered the lowly expressed genes, it worked out fine. Thanks!