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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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Error in CreateSinglerSeuratObject #30

Open mengchengyao opened 5 years ago

mengchengyao commented 5 years ago

Hi, thanks for developing SingleR. Great tool! When i created object with CreateSinglerSeuratObject，

singler = CreateSinglerObject(dir/10X/mm10, annot = NULL, "test", min.genes = 0,technology = "10X", species = "Mouse", citation = "", normalize.gene.length = F, variable.genes = "de",fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T, reduce.file.size = T, numCores = SingleR.numCores) [1] "test" [1] "Reading single-cell data..." [1] "Create Seurat object..." Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Regressing out: nUMI |======================================================================| 100%Error in { : task 1 failed - "incorrect number of dimensions"

I get error with "in { : task 1 failed - "incorrect number of dimensions"." I also tryied counts file, get the same Error.

Best Wishes

dviraran commented 5 years ago

Thanks!

The failure seems to be still in the generating of the Seurat object. Can you post a small version of the counts matrix (~20 cells)?

mengchengyao commented 5 years ago

Thanks!

The failure seems to be still in the generating of the Seurat object. Can you post a small version of the counts matrix (~20 cells)?

Thanks! I tryied, but failed. [1] "test" [1] "Reading single-cell data..." [1] "Create Seurat object..." Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Regressing out: nUMI |======================================================================| 100%Error in { : task 1 failed - "incorrect number of dimensions"

my counts matrix

head(as.matrix(expressionmatrix)[1:1000,1:10]) AAACCTGAGAGCCCAA AAACCTGCAGCTATTG AAACCTGCAGCTGGCT AAACCTGCAGTCAGAG Xkr4 0 0 0 0 Gm1992 0 0 0 0 Gm37381 0 0 0 0 Rp1 0 0 0 0 Rp1.1 0 0 0 0 Sox17 0 0 0 0 AAACCTGTCAACCATG AAACCTGTCACAACGT AAACCTGTCAGCTTAG AAACCTGTCCGTTGCT Xkr4 0 0 0 0 Gm1992 0 0 0 0 Gm37381 0 0 0 0 Rp1 0 0 0 0 Rp1.1 0 0 0 0 Sox17 0 0 0 0 AAACCTGTCTCAACTT AAACCTGTCTGCTTGC Xkr4 0 0 Gm1992 0 0 Gm37381 0 0 Rp1 0 0 Rp1.1 0 0 Sox17 0 0

Best Wishes

dviraran commented 5 years ago

you need to save it as a file and upload it.

mengchengyao commented 5 years ago

you need to save it as a file and upload it.

Thanks! I dit it as you said, but failed. Howerver I passed by another way, I used CreateSinglerObject function and seurat object without CreateSinglerSeuratObject function, and I get what I wanted!

Best Wishes