reached iteration limit in SCTransform

Question

[re_raz]

Hi I got hundreds of warning "reached iteration limit" when I run

Sproject <- SCTransform(Sproject, vars.to.regress = c("percent.mt", "percent.rps", "percent.rpl", "percent.rrna", "nCount_RNA", "nFeature_RNA"), verbose = FALSE, return.only.var.genes = FALSE)

and the warning not stop until I stop running the code. Does anyone face the same issue? Is there any solution?

What is alternative function to replace SCTransform?

Thanks

Answer 1

[rpolicastro]

This error is related to a problem with parameter estimation (theta) on certain cells when fitting the negative binomial regression. I've run into this problem before, and I found a few issue responses from the authors of Seurat/SCTransform that these warnings can be ignored, because that parameter is not used downstream (due to parameter regularization). More info about this in the github issues here and here.

[re_raz]

Thank you for help, but the warning not stop and I have to stop the code

[rpolicastro]

You can ignore the warnings. Let the code run and it should eventually finish.

[re_raz]

I will try that, Thanks

[re_raz]

Not working for me, and I got a message Error: cannot allocate vector of size 18 GB although I am running my code on a remote server and memory.limit() give Inf.

[rpolicastro]

Are you sure your remote server has no memory limit?

[re_raz]

I check by memory.limit() and give me Inf