Error using FindMarkers

[mplass]

Hi,
if I try to use the negative binomial test in the function FindAllMarkers it crashes.

Example:
all.markers <- FindAllMarkers(nbt, only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25,test.use = "negbinom")
| | 0 % ~calculating Error in while ((it <- it + 1) < limit && abs(del) > eps) { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In [<-.data.frame(*tmp*, , "GENE", value = list(plan2_AAGCAGATTAAA = 2, :
provided 9930 variables to replace 1 variables

Thanks,

[davidhbrann]

I also just got the same error when using either FindMarkers or FindMarkersNode with "negbinom":
"FindMarkers"
Error in while ((it <- it + 1) < limit && abs(del) > eps) { :
missing value where TRUE/FALSE needed
Calls: FindMarkers ... lapply -> FUN -> summary -> glm.nb -> as.vector -> theta.ml
In addition: Warning message:
In [<-.data.frame(*tmp*, , "GENE", value = list(DS11TCCTTATTTCAG = 6L, :
provided 6207 variables to replace 1 variables

[satijalab]

If you could provide some sample data that recreates this error or the object itself, that would be helpful. Can't seem to reproduce it on the datasets I have.

[andrewwbutler]

Resolved the bug. Reinstalling should allow you to run any of the marker detection functions with the "negbinom" test without problems.