error of addGeneIntegrationMatrix : <simpleError in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent>

[XiaoKaixuan12333]

ArchR-addGeneIntegrationMatrix-171f8742a45cc6-Date-2023-12-01_Time-16-51-22.log This is an issue template made by the developers of ArchR. You MUST follow these instructions.

HI, when i use addGeneIntegrationMatrix , i meet the question of <simpleError in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent> ，i have been used other method mentioned like set the defaultassay of seurat object, but it is not work. so i would like to know how to fix it.

[rcorces]

Hi @XiaoKaixuan12333! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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[igunduz]

Hello @XiaoKaixuan12333, I keep receiving the same error. Have you been able to solve this?

[igunduz]

Hello again @rcorces @XiaoKaixuan12333 ,

The issue is due to Seurat's RunCCA function, by updating Seurat V5 I was able to fix the problem

[BartBryant]

Hello @igunduz , I also initially had the 'dn: length of 'dimnames' error I then updated to Seurat v5 and now get Warning: Data is of class dgeMatrix. Coercing to dgCMatrix. Error in slot(object = object, name = "features")[[layer]] <- features : more elements supplied than there are to replace

Any thoughts?

[igunduz]

Hello @igunduz , I also initially had the 'dn: length of 'dimnames' error I then updated to Seurat v5 and now get Warning: Data is of class dgeMatrix. Coercing to dgCMatrix. Error in slot(object = object, name = "features")[[layer]] <- features : more elements supplied than there are to replace

Any thoughts?

Hello, I also received the same error and, testIntegration function from here solved the problem for me