satijalab/sctransform

Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : cell attribute "log_umi" contains NA, NaN, or infinite value

LooLipin opened this issue · 2 comments

LooLipin commented

Hi there,

This is a follow up to my comment on #131 (comment)

I was able to successfully run 7 of my 8 visium samples by following the vignette on https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html

Unfortunately, one failed at the scTransform stage with Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : cell attribute "log_umi" contains NA, NaN, or infinite value

I tried to upload my object but it is slightly over the limit. Can you please provide me with an email to forward?

Thanks,
Lipin

saketkc commented

You can email me at schoudhary@nygenome.org

saketkc commented

One of your cell has no UMIs:

> min(obj$nCount_Spatial)
0

You can filter the cell out:

obj <- subset(obj, nCount_Spatial>0)

and then run SCTransform:

obj <- SCTransform(obj, assay="Spatial", vst.flavor="v2")
  • 👍8