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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Error in dimnames(x) <- dn #253

Closed XYZ-NCI closed 2 years ago

XYZ-NCI commented 4 years ago

Hi, Thank you for this wonderful tool. It has been extremely helpful. In the past, I have been using the tool with minimal problem. However, there is one recent sample (10x single cell RNAseq) that I constantly ran into this same error message:

Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Calls: ... -> removeCNV -> removeCNV -> colnames<- Execution halted

I suspect it has something to do with the low CNV event detected in this sample but I would like to get your input in this...

Here is the code I used:

infercnv_obj_PNF_CS026099 = infercnv::run(infercnv_obj_PNF_CS026099, cutoff=0.1, out_dir="cluster_by_group_PNF_CS026099", cluster_by_groups=TRUE, denoise=TRUE, HMM=TRUE)

And attached is the .r.out file for your reference.

Thank you very much!

Screen Shot 2020-08-24 at 11 29 01
GeorgescuC commented 4 years ago

Hi @XYZ-NCI ,

The error does look like it is linked to not finding any cnv to remove when doing the filtering (as it only finds 1). A quick workaround for this case should be to disable the Bayesian filtering (as nothing gets filtered out anyway) by adding BayesMaxPNormal=0 to the options. Which version of infercnv are you using?

Regards, Christophe.