dimnames error in CreateSinglerObject

[z5ouyang]

Thanks for developing this tools. I am following the case 2. by providing the member of the Seurat object (X): Do you have any suggestion?

singler <- CreateSinglerObject(as.matrix(X@raw.data), annot = NULL, project.name="Lung10X",min.genes = 0,

• technology = "10X", species = "Mouse", citation = "",
• ref.list = list(), normalize.gene.length = F, variable.genes = "de",
• fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T,
• reduce.file.size = T, numCores = 32) [1] "Dimensions of counts data: 17620x16043" [1] "Annotating data with Immgen..." [1] "Variable genes method: de" [1] "Number of DE genes:3400" [1] "Number of cells: 16043" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 25:06 [1] "Number of DE genes:3400" [1] "Number of clusters: 10" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:01 [1] "Annotating data with Immgen (Main types)..." [1] "Number of DE genes:2231" [1] "Number of cells: 16043" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 02:10 [1] "Number of DE genes:2231" [1] "Number of clusters: 10" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:01 [1] "Annotating data with Mouse-RNAseq..." [1] "Variable genes method: de" [1] "Number of DE genes:3630" [1] "Number of cells: 16043" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:34 [1] "Number of DE genes:3630" [1] "Number of clusters: 10" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:01 [1] "Annotating data with Mouse-RNAseq (Main types)..." [1] "Number of DE genes:2871" [1] "Number of cells: 16043" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:30 [1] "Number of DE genes:2871" [1] "Number of clusters: 10" [1] "Fine-tuning round on top cell types (using 32 CPU cores):" |======================================================================================================================| 100%, Elapsed 00:01 Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

[z5ouyang]

After many tries, it seems like the parameter "clusters" can NOT be NULL, I provide the Seurat "X@ident" to "clusters", then it successfully complete. Guess it is a temporal solution.

[dviraran]

Thanks for sharing this. I am not sure where the issue comes from since it seems it was able to use the SingleR clusters in both references, and the error comes only later. However, there is no use of clusters afterward in the code.