Warning: there are only 5 potential marker genes in CellMatch database for Mouse on Skin!

[Tommaso12]

Hello, I might still have the same problem as before. Here the code I used.Do you think is correct?

Thanks a lot for the help!

library(Seurat)
library(cowplot)
library(gplots)
library(dplyr)
library(ggplot2)
library(openxlsx)
library(slingshot)
library(SingleCellExperiment)
library(destiny, quietly = TRUE)
library(clusterExperiment)
library(tidyverse)
library(scCATCH)

#load RDS
IMQ.integrated <- readRDS("/srv/workspace/rprojects/tgastaldi/Liu_2020_scRNAseq/IMQ.integrated.rds")
top10.IMQ.integrated <- head(GetAssayData(IMQ.integrated), 10)

matrix.IMQ.integrated <- GetAssayData(IMQ.integrated, slot = "scale.data")

matrix.IMQ.integrated <- rev_gene(matrix.IMQ.integrated, data_type = "data", species = "Mouse", geneinfo = geneinfo)
## Revising gene symbols for data matrix 
## ***Done***

x <- Idents(IMQ.integrated)
all(colnames(matrix.IMQ.integrated)== names(x))
## [1] TRUE
x <- as.character(x)

IMQ.integrated.CATCH <- createscCATCH(matrix.IMQ.integrated, cluster = x)

IMQ.integrated.CATCH <- findmarkergene(IMQ.integrated.CATCH, 
                                      species = "Mouse",
                                      cluster = "All",
                                      marker = cellmatch,
                                      cancer = "Normal",
                                      tissue = "Skin",
                                      use_method = "1",
                                      #cell_min_pct = 0.25,
                                      #logfc = 0.25,
                                      #pvalue = 0.05
                                      )
## Warning: there are only 5 potential marker genes in CellMatch database for Mouse on Skin!
## Error in if (nrow(ndata) == 0) {: Argument hat Länge 0
IMQ.integrated.CATCH <- findcelltype(IMQ.integrated.CATCH)
## Error in findcelltype(IMQ.integrated.CATCH): No marker genes found!

[multitalk]

Hello, you can try to select more relevant tissues in cellmatch or you can construct a custom data.frame with your collected marker genes.

[Tommaso12]

Hello, thanks for the suggestion. I will give it the try. I am actually trying now to construct a data.frame collecting annotations from different databases as Immgen. Let's see...