runSCENIC_3_scoreCells.R Line84 non-numeric error

[wang-research]

Hi,

I found line 83-84 of runSCENIC_3_scoreCells.R:

trhAssignment <- getThresholdSelected(cells_AUCellThresholds)
trhAssignment <- signif(trhAssignment,3)

The 83-line gave a 'list' result, but 'signif' needs a numeric input?
By the way, there are some 'NA' names in 'cells_AUCellThresholds'. Coud I simply delete theme items?

Thank you, sincerely.

[jaimicore]

Hi

I had the same problem but I fixed it with the following change:

## Original line:
trhAssignment <- signif(trhAssignment,3)

Changes:
trhAssignment <- as.list(signif(unlist(trhAssignment), 3))

You should pass the argument as a vector, in order to apply the signif function, then you can convert the resulting vector in a list.

[wang-research]

Thanks! I fixed it.

[danjong99]

Hi,

I had a same issue.
My question is how you fixed the problem in detail.
Did you change the line from runSCENIC_3_scoreCells.R file? and re-install the whole package?
or you newly define runSCENIC_3_scoreCells function only in R and used it?
I am trying either way but, none of them are working properly.

if you can describe more in detail, it would be very helpful.

[jaimicore]

I modified the code in runSCENIC_3_scoreCells.R

After that, in R:

detach("package:SCENIC", unload = TRUE); remove.packages("SCENIC")

Then compress the file and compile it from the command line:
R CMD INSTALL SCENIC.tar.gz

[afaissa]

Hi,

I had a same issue.
My question is how you fixed the problem in detail.
Did you change the line from runSCENIC_3_scoreCells.R file? and re-install the whole package?
or you newly define runSCENIC_3_scoreCells function only in R and used it?
I am trying either way but, none of them are working properly.

if you can describe more in detail, it would be very helpful.

Hi,

Did you figure out this issue? I have the same problem as you. Can you help me?

[rach226a]

Hi,

I believe the issue is related to parallelization within the AUCell_exploreThresholds() function (of runSCENIC_3_scoreCells). It seems like some of the cores are outputting NA. If you run AUCell_exploreThresholds() many times, different regulons will be replaced by NA value each time. It seems to work if you lower your nCores or set nCores = 1 (safest option!). I hope this helps anyone who runs into this issue!