Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array of at least two dimensions

[corticaltone]

Hi
I'm trying to run inferCNV on 10x genomics data and keep getting the following error message
INFO [2020-12-09 11:45:38] Adding h-spike
INFO [2020-12-09 11:45:38] -hspike modeling of Epithelial_C5
Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) :
'x' must be an array of at least two dimensions

I read through Issue #156 but was not able to find a solution there. Here is the full output:

infercnv_obj = infercnv::run(infercnv_obj,

•                          cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
  

•                          out_dir=tempfile(), 
  

•                          cluster_by_groups=TRUE, 
  

•                          denoise=TRUE,
  

•                          HMM=TRUE,
  

•                          resume_mode = FALSE)
  

INFO [2020-12-09 11:38:53] ::process_data:Start
INFO [2020-12-09 11:38:53] Creating output path /var/folders/sq/fdhpv_c14b514x7q1ygn2mgc0000gp/T//RtmpBLfKfH/file451d3b86438b
INFO [2020-12-09 11:38:53]

STEP 1: incoming data

INFO [2020-12-09 11:41:02]

STEP 02: Removing lowly expressed genes

INFO [2020-12-09 11:41:02] ::above_min_mean_expr_cutoff:Start
INFO [2020-12-09 11:41:07] Removing 8916 genes from matrix as below mean expr threshold: 0.1
INFO [2020-12-09 11:41:13] validating infercnv_obj
INFO [2020-12-09 11:41:13] There are 9352 genes and 43972 cells remaining in the expr matrix.
INFO [2020-12-09 11:42:06] no genes removed due to min cells/gene filter
INFO [2020-12-09 11:44:23]

STEP 03: normalization by sequencing depth

INFO [2020-12-09 11:44:23] normalizing counts matrix by depth
INFO [2020-12-09 11:45:37] Computed total sum normalization factor as median libsize: 3570.000000
INFO [2020-12-09 11:45:38] Adding h-spike
INFO [2020-12-09 11:45:38] -hspike modeling of Epithelial_C5
Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) :
'x' must be an array of at least two dimensions

[corticaltone]

In case this is helpful:

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

InferCNV version 1.4.0

[Momomocheng]

In annotations_file of CreateInfercnvObject() ，you'd better make each label in annotations_file has at least two cells.
when reRun the infercnv::run method, delete those files generated last time.
That works for me.

[qins]

Try to remove this line:
"HMM=TRUE"

[GeorgescuC]

Hi ,

Annotation groups are indeed expected to have more than 1 cell as it does not make sense to have a unique cell of a given type sequenced when taking into account the level of noise present in single cell data.

Regards,
Christophe.

[mailmrcai]

In annotations_file of CreateInfercnvObject() ，you'd better make each label in annotations_file has at least two cells. when reRun the infercnv::run method, delete those files generated last time. That works for me.

this works for me