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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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CreateBigSingleRObject Error #74

Open ishanparanjpe opened 5 years ago

ishanparanjpe commented 5 years ago

Hi, Thank you for this great package. I am running CreateBigSingleRObject for a dataset with ~22000 cells singler <- CreateBigSingleRObject(data.combined@assays$SCT[,rownames(annot)], annot = annot[,1], project.name="test", min.genes = 200, technology = "10X", species = "Human", citation = "",N = 5000, ref.list = list(), normalize.gene.length = F, variable.genes = "de", fine.tune = T, reduce.file.size = T, do.signatures = T,do.main.types = T, numCores = SingleR.numCores) It looks like all of the fine tunings step work but then I get this error: [1] "Annotating data with Blueprint_Encode (Main types)..." [1] "Number of DE genes:3006" [1] "Number of cells: 2738" [1] "Fine-tuning round on top cell types (using 3 CPU cores):" |=======================================================================| 100%, Elapsed 02:22 [1] "Number of DE genes:3006" [1] "Number of clusters: 10" [1] "Fine-tuning round on top cell types (using 3 CPU cores):" |=======================================================================| 100%, Elapsed 00:00

Error in singler$singler[[j]]$SingleR.single$labels[order, ] :

subscript out of bounds

dviraran commented 5 years ago

Hi,

First, depending on the machine you are working with of course, but I ran SingleR for 20K cells on my macbook and it worked fine. Not sure you really need the CreateBigSingleRObject function.

Second, what happens is that there is some discrepancy between how SingleR and how Seurat filter cells. Easiest fix here is to use min.genes=0 and SingleR will not filter any cell.

Third, as input for SingleR don't use SCT, use the RNA field. SCT filters out many genes, you don't want that.

Best, Dvir

ishanparanjpe commented 5 years ago

Hi, Thanks for your help. When I try to plot a tsne plot after running CreateBigSingleRObject, I get this error. It seems like the cellnames attribute is NA. out = SingleR.PlotTsne(singler$singler[[1]]$SingleR.single.main, singler$meta.data$xy,do.label = T, do.letters = F,labels=singler$singler[[1]]$SingleR.single.main$labels, dot.size = 2,label.size = 5,alpha=0.5 )

Error in data.frame(row.names = SingleR$cell.names) : row names contain missing values

dviraran commented 5 years ago

If thats true (that cell.names is NA), then something has failed in the process. This shouldn't happen.