ArchR
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GreenleafLab
issue with integrating scRNAseq with ArchR using 'addGeneIntegrationMatrix( )
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
