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YosefLab / VISION

Signature Analysis and Visualization for Single-Cell RNA-seq
https://yoseflab.github.io/VISION/
MIT License
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Error in x$consistency : $ operator is invalid for atomic vectors #133

Open yfei-w opened 3 months ago

yfei-w commented 3 months ago

Hi there! I am running VISION using Seurat object and it was working fine before but I am now encountering error:

sig <- c("gene_sets/GO_ALPHA_BETA_T_CELL_ACTIVATION.gmt")
vis <- Vision(Seurat_obj, dimRed ="umap", signatures = sig, projection_methods = NULL)
vis <- analyze(vis)
  |=======================================================================================| 100%, Elapsed 00:00
  |=======================================================================================| 100%, Elapsed 00:00
  sigSize sigBalance
1      43          1
  |=======================================================================================| 100%, Elapsed 00:00
  |=======================================================================================| 100%, Elapsed 00:16
  |=======================================================================================| 100%, Elapsed 01:56
  |========================                                                                   |  26%, ETA 00:01
Warning: all scheduled cores encountered errors in user codeError in x$consistency : $ operator is invalid for atomic vectors

I believe this might because of the input Seurat object but I compared the ones that worked and the ones don't work and I could not find out what is causing the error. Would it be possible that you could point me to the right direction in how to fix the input or anything that would fix this issue? Thanks!!