Issue in findmarkergene function
s-yadav21 opened this issue · 5 comments
First of all, thank you for creating this package for single cell annotation.
I was trying to annotate my single cell dataset using you package and encountered following error:
clu_markers <- findmarkergenes(dif.PAC, species = "Human", cluster = 'All', match_CellMatch = TRUE, cancer = "Pancreatic Ductal Adenocarcinomas", tissue = "Pancreas", cell_min_pct = 0.25, logfc = 0.25, pvalue = 0.05)
`Note: the raw data matrix includes 14308 cells and 19823 genes.
---Revising gene symbols according to NCBI Gene symbols (updated in June 19, 2020, https://www.ncbi.nlm.nih.gov/gene) and no matched genes and duplicated genes will be removed.
Note: the new data matrix includes 14308 cells and 16587 genes.
Warning: there are only 1 potential marker genes in CellMatch database for Human Pancreatic Ductal Adenocarcinomas on Pancreas!
Error in if (nrow(ndata) == 0) { : argument is of length zero`
I am using a normalized Seurat object with cluster details. Could you please let me know what could be possible wrong?
I‘m so sorry for my delay in writing back, but I've been very busy working recently. Actually this is because there are only 1 potential marker genes in CellMatch database. You can try v3.0 now since it allows you to use different combination of tissues to generate more potential marker genes.
Hi All,
I was trying to annotate my single cell data using scCATCH package but I encountered this following error:
code: clu_markers <- findmarkergenes(object = pbmc, species = 'Mouse', cluster = 'All', match_CellMatch = TRUE, cancer =
NULL, tissue = NULL, cell_min_pct = 0.25, logfc = 0.25, pvalue = 0.05)
error: Error in findmarkergenes(object = pbmc.data, species = "Mouse", cluster = "All", :
could not find function "findmarkergenes"
Note: I have already used the package to annotate this same data, but when I rerun the code I keep on facing this issue. Could you possibly tell me where I am going wrong?
Hello, you can re-install scCATCH v3.0 and follow the user guide.
Firstly thank you for helping me. I re-installed the package, but it now shows an error:
Error in findmarkergene(object = pbmc, species = "Mouse", cluster = "All", :
unused argument (match_CellMatch = TRUE)
Some parameters have been changed. No cluster exists. You can try the following code：
obj <- findmarkergene(object = pbmc, species = "Mouse", marker = cellmatch, tissue = "Blood")