Difficulty running updateCutoffs() on tutorial (simulated) data

[kmuench]

Hello, Thank you very much for creating and maintaining this resource! I really appreciate the work to help standardize the use of these tools in biological data types.

I just started a new project and am getting this error message when I run the updateCutoffs command in the main README tutorial:

Error in FDR$randcounts/FDR$truecounts : 
  non-numeric argument to binary operator

I'm in the process of trying it with my own data. I can verify that in both cases the pr@results$propr is numeric. I get the same error for a range of values of number_of_cutoffs and tails, or if I use clr or iqlr.

Do you have any ideas what might be happening here? Kristin

[patrick-cannon]

Hi Kristin,

I am getting the same error. Did you end up getting the tutorial to work? Or at least, is your own data working?

[laugior]

Try this:

pr <- updateCutoffs(
        pr,
        number_of_cutoffs = 100,  # number of cutoffs to estimate FDR
        custom_cutoffs = NA,  # replace NULL with NA
        tails = 'right',  # consider only the positive values ('right') or both sides ('both')
        ncores = 4  # parallelize here
      ) 

or this

pr <- updateCutoffs(
        pr,
        number_of_cutoffs = 100,  # number of cutoffs to estimate FDR
        tails = 'right',  # consider only the positive values ('right') or both sides ('both')
        ncores = 4  # parallelize here
      ) 

[suzannejin]

Hello @kmuench! Sorry for the late answer. There was an error in the README, it should be custom_cutoffs = NA just as @Tiltedkid replied!