-
Notifications
You must be signed in to change notification settings - Fork 126
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Unconstrained integration error - "more elements supplied than there are to replace" #2136
Comments
Hi @LacquerHed! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other |
Hi @LacquerHed I had the same error, in the same step. This is my code (the part that generates the error) seRNA = readRDS("scRNA-Hematopoiesis-Granja-2019.rds")
seurObj = CreateSeuratObject(counts = CreateAssayObject(assay(seRNA)), meta.data = as.data.frame(colData(seRNA)))
Project = addGeneIntegrationMatrix(
ArchRProj = Project,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "IterativeLSI",
seRNA = seurObj,
addToArrow = FALSE,
groupRNA = "BioClassification",
nameCell = "predictedCell_Un",
nameGroup = "predictedGroup_Un",
nameScore = "predictedScore_Un"
) I was running on R-4.3.2 with ArchR-1.0.2. |
Try update your And try to run |
I have once been doubted by the same error but it works with latest |
Hi I am running unconstrained integration and getting the following error, which seems to stem from the slots/layers ArchR is pulling from the seRNA (Seurat object) input.
2024-03-14 12:11:53.67366 : Block (1 of 1) : Imputing GeneScoreMatrix, 0.323 mins elapsed. Getting ImputeWeights 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
This is happening with Seurat V5 objects but also V4 when I downgraded to that, so not sure if its the new layer structure of Seurat V5. Not sure how to limit elements supplied from the seRNA. Thanks.
ArchR-addGeneIntegrationMatrix-129a04b8342d3-Date-2024-03-14_Time-12-11-30.735514.log
The text was updated successfully, but these errors were encountered: