Seurat V5 and cosg

[liyanguo520]

Is there any way to solve the problem?

marker_cosg <- cosg(scRNA_object, groups='all',assay='SCT',

•                 slot='data',mu=1,n_genes_user=100,
  

•                 remove_lowly_expressed=TRUE,
  

•                 expressed_pct=0.1)
  

Error in ..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L]) : NA subscripts in x[i,j] not supported for 'x' inheriting from sparseMatrix addition: Warning message: x or y has vectors with all zero; consider setting use_nan = TRUE to set these values to NaN or use_nan = FALSE to suppress this warning

[genecell]

Hi,

The above error might be caused by using the SCT assay, which is not sparse after the scTransform normalization. We recommend use the RNA assay with the slot data as the input. Hope it works!

Best, Min