Error in data.frame(C = consistency, pValue = pvals, FDR = fdr) : arguments imply differing number of rows: 1, 0

[wchenqi]

I tried rds <- sc.metabolism.Seurat(obj = rds, method = "VISION", imputation = F, ncores = 2, metabolism.type = "REACTOME")
but it returned an Error information, I've no idea what it means, please help me.

Your choice is: REACTOME
Start quantify the metabolism activity...
Loading data from /work/med-wangcq/miniconda3/envs/scRNA/lib/R/library/scMetabolism/data/REACTOME_metabolism.gmt ...

Using 15133/31053 genes detected in 0.10% of cells for signature analysis.
See the sig_gene_threshold input to change this behavior.

Beginning Analysis

Computing a latent space for expression data...

Determining projection genes...
Applying Threshold filter...removing genes detected in less than 1439 cells
Genes Retained: 9117
Applying Fano filter...removing genes with Fano < 2.0 MAD in each of 30 bins
Genes Retained: 1724

Clustering cells...
Using latent space to cluster cells...
completed

Projecting data into 2 dimensions...
Running method 1/1: tSNE30 ...

Evaluating signature scores on cells...

Creating 0 background signature groups with the following parameters:
sigSize sigBalance
signatures per group: 3000
'as(, "dgeMatrix")' is deprecated.
Use 'as(as(as(., "dMatrix"), "generalMatrix"), "unpackedMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Computing KNN Cell Graph in the Latent Space...

Evaluating local consistency of signatures in latent space...

|=======================================================================================================| 100%, Elapsed 00:00
Error in data.frame(C = consistency, pValue = pvals, FDR = fdr) :
arguments imply differing number of rows: 1, 0

[wanwan26]

I had this problem too.

[chenliji]

Do you know how to solve it?

[TIPPLERXIE]

I encountered the same error. Does anyone else know how to fix it?