Bioinformatics: Findstates command in celltrails not working

Question

[tom5]

Hi, I am performing an scRNAseq analysis. I am using the findstates command in cell trails but it is returning an error. Here is the code and error results. Unfortunately, I am not sure how to resolve this, and all the previous commands work. I would provide my full code and data, but don't think biostars allows uploads.

Command: cl <- findStates(smith_data, min_size=0.01, min_feat=5, max_pval=1e-4, min_fc=2)

Error: Initialized 23 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Error in Si.fcn(ni = ni, di = di, surv.est = surv.est) :
  dims [product 5] do not match the length of object [6]
In addition: Warning messages:
1: 'isSpike' is deprecated.
See help("Deprecated")
2: In ni - di :
  longer object length is not a multiple of shorter object length

[Mensur Dlakic]

I appreciate the effort to help catalog the questions by subject, but it may be slightly redundant to title your posts using Bioinformatics: on a website with a Bioinformatics explained tag. It kind of feels like writing on Simply Recipes and titling your post "Cooking: Is it possible to make a Hollandaise sauce without eggs?"

[tom5]

Thanks! Will avoid this for future posts. Do you have any insight into the celltrails issue? This is the resource: https://dcellwanger.github.io/CellTrails-handbook/clustering.html#hierarchical-spectral-clustering