Error in FindClustersRecall: missing value required for stats::runif < prop.zero

[wong-nw]

When working with a previous object containing RNA, SCT, and integrated assays, the object is set up to analyze clusters on the integrated assay. Running FindClustersRecall produces the following output:

so_recall = FindClustersRecall(so)
Pulling data from Seurat object
Computing artificial features
Error in if (stats::runif(1) < prop.zero) { : 
  missing value where TRUE/FALSE needed

Do you know if this is an internal bug or an issue with the data set itself?

[agdenadel]

@wong-nw are you able to share your data with me (even privately)? I am a bit busy because I am defending my PhD on Thursday, but after that I would be happy to look into this. I worked directly with RNA assays during development so I am not too surprised that something like this happened. It's most likely a bug and not an issue with the data.

Also, recall doesn't yet have any built-in support for integrated data so I'm not sure how the integrated result will turn out. Which integration method did you use?

[agdenadel]

@wong-nw circling back to this, I am happy to look into this for you. Can you help me reproduce this error?

[wong-nw]

Hi @agdenadel, sorry about the delay. This particular dataset used the "integrate" function from Seurat, which, if I recall correctly, is CCA. I don't have permission to share this data, as it is still unpublished, but I can try to use some public datasets to reproduce the error.

From what I can interpret, it looks like the error starts with the insertion of the pseudodata (my terminology is probably wrong), which would make sense, since the integrated assay only contains the variable genes (~3000).

I'll reach out with a test dataset/code soon.

Good luck on your dissertation defense! Been there, done that, and eventually got the degree in the end