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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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reached iteration limit #82

Closed Pinpin-u1111 closed 3 years ago

Pinpin-u1111 commented 3 years ago

I have this message repeatedly in the console after launching "sctransform::vst(cd8.data, latent_var = c("log_umi"), return_gene_attr = TRUE, return_cell_attr = TRUE, verbosity = 1)" with cd8.data being a large dgCMatrix of 9,941 features on 22,383 cells. R keeps running and I have to escape from the process. Has anybody a clue? Thanks a lot in advance

ruqianl commented 3 years ago

Duplicate of #25

Pinpin-u1111 commented 3 years ago

ChristophH/sctransform#25 is not solving the problem: it advises to ignore the warning. However, I cannot as the message is returned continuously until I force stop the run.

ChristophH commented 3 years ago

With 22k cells the call to vst should finish within a few minutes. Perhaps printing all those warnings slows things down, but the command should eventually return something.

You could also try:

  1. A method that does not use theta.ml internally (method = 'qpoisson' or method = 'glmGamPoi')
  2. Wrapping the vst call in suppressWarnings()
Pinpin-u1111 commented 3 years ago

Thank you! I used the suppressWarnings() and got the result in a few minutes