issue with integrating scRNAseq with ArchR using 'addGeneIntegrationMatrix( )

[BartBryant]

My error comes from step 8.1 from 'Full Manual', specifically I am getting the error <simpleError in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent> after running projAVF <- addGeneIntegrationMatrix( ArchRProj = projAVF, useMatrix = "GeneScoreMatrix", matrixName = "GeneIntegrationMatrix", reducedDims = "IterativeLSI", seRNA = avfSham.combined, addToArrow = FALSE, groupRNA = "celltype.AVF", nameCell = "predictedCell_Un", nameGroup = "predictedGroup_Un", nameScore = "predictedScore_Un" )

I looked at ArchR's 'Issues' and found others resolved the issue with remove.packages("SeuratObject") packageurl <- "http://cran.r-project.org/src/contrib/Archive/SeuratObject/SeuratObject_4.1.3.tar.gz" install.packages(packageurl, repos=NULL, type="source")

but I still got the same error message when trying to integrate my scATACseq and scRNAseq data with ArchR

any advice? Thanks bart

[rcorces]

Hi @BartBryant! 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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[BartBryant]

i was able to resolve the same issue you had by removing current SeuratObject and installing SeuratObject_4.1.3 running with Seurat_4.3.0 thanks to @dgagler! refer to issue#2042 and #2040

[sudeepthi5]

I got the same error even for the example data used in the pipeline, can anyone help with this. Thank you