Error in as.matrix(adata@assays$RNA@scale.data)[markers, ] : subscript out of bounds

[xiangyupan]

Hi anyone,

It's so exciting for the excellent package calculating cell differential potency. But when an error happened when I run the codes following the GitHub.

As the scRNA-seq is the limb regeneration data of axolotl. I replace the cell cycle genes by re-input the axolotl gene ID. My code is as follows:

Hope for your reply. Thank you very much.

[xiangyupan]

Hi @kma2112
I have tried another method when running run_stemFinder by replacing method = 'stdev', it works well. Although I still can not resolve the question above, but I have got the stemFinder score. Still hope for your reply.

[kma2112]

Thank you for using this tool!

First, let's make sure that all of the genes in your cell cycle gene list inputted to run_stemFinder are included in your counts matrix so the subsetting step does not return an out of bounds error. It looks like you selected for only cell cycle genes in the data, however, but would you mind double checking length(cell_cycle_genes[cell_cycle_genes %in% rownames(as.matrix(adata@assays$RNA@scale.data))]) ?

Is your data scaled (can you print the first five rows and columns of adata@assays$RNA@scale.data for me)?

Finally, would you mind sharing your sessionInfo()? Thank you!