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aertslab / AUCell

AUCell: score single cells with gene regulatory networks
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All zeros for regulon's AUC #2

Closed topherconley closed 5 years ago

topherconley commented 6 years ago

Hi,

I ran pySCENIC's workflow to generate AUC values followed by AUC_exploreThresholds from the latest version (1.2.4) of AUCell.

cells_assignment <- AUCell_exploreThresholds(auc,plotHist=F, assign=TRUE, nCores = 30, verbose = T)

which results in this error.

Error in { : task 386 failed - "missing value where TRUE/FALSE needed"

It turns out that the regulon with index 386 had all zeros for the AUC.

I recommend removing this regulons from consideration or at least issue a warning so other users don't get tripped up on this. By the way, is it possible that some assumption is being violated in the calculation of AUC when you notice a regulon has an AUC of all zeros?

All the best, Chris

s-aibar commented 5 years ago

Thank you, This is now solved in newer versions of the packages.