[ERROR] Invalid Counts data

[cyanching]

Hey there! I am new to cellphonedb, I have tried to export my normalised count data into the same format as the example you have then run the statistical_analysis method on my meta and count files, but I keep getting the error: Invalid Counts data, I have called count data from my Seurat object, then wrote a txt table:

human_count <- human.Seurat@assays$RNA@counts %>% as.data.frame() %>% rownames_to_column() %>% rename(Gene = rowname)

write.table(human_count,"human_count_integrated_30PC.txt",sep="\t")

Is there anything I did wrong? Could you suggest a solution?

[keenhl]

Is the column order in the counts file the same as the row order in the meta file?

[cyanching]

Hey keenhl, thank you for your reply! I already solved the issue by adjusting the formating of my count file!

[keenhl]

Good. Thanks for the update.

[singcell]

@cyanching Can you share how your formatting solved the problem. i have the same issue.

[cyanching]

@cyanching Can you share how your formatting solved the problem. i have the same issue.

I corrected the format of my count file, so I have (1,1) as 'Gene', then filed the first col with ensemble gene ID, the first row with cell ID, the rest with count data.

[zhanglab2008]

@cyanching Can you share how your formatting solved the problem. i have the same issue.

I corrected the format of my count file, so I have (1,1) as 'Gene', then filed the first col with ensemble gene ID, the first row with cell ID, the rest with count data.

Great tip! I also had the same error when I ran the codes from the Nature Protocol paper. I solved it using your methods. Thanks!