Error when running SingleR.combine

[mbassalbioinformatics]

Hi

When running singleR.combine on a multiple singler objects i get 1: In rbind(singler$singler[[j]]$SingleR.single.main$pval, singler.list[[i]]$singler[[j]]$SingleR.single.main$pval) : number of columns of result is not a multiple of vector length (arg 2)

Ive updated to the latest version and still getting the same problem. Suggestions please?

All im running is singler_combined = SingleR.Combine( singler_objects, order = colnames(combined_normalized_counts) )

[dviraran]

not sure why using there rbind at all. pval is a vector. I changed it in the code and deployed it. can you update SingleR and test it again?

[mbassalbioinformatics]

Thanks for the prompt fix! Seems to have worked for fixing that error.

I now get a different warning however -

Warning messages:
1: In cor(cell.type.classification$cell.types.avg[A, ], as.matrix(sc.data[A,  :
  the standard deviation is zero

Although this doesnt seem to break the code as before... suggestions??

[dviraran]

This is probably because one (or more) of the cells have all zeros in the genes that are used for this classification (Kang et al.). Nothing to worry about.

[mbassalbioinformatics]

ok thanks!