Seurat: IntegrateData error v3 lastest pull "Attempting to add a different number of cells and/or features"

[fidelram]

Using a fresh installation of Seurat3 (from today) I get the following error when following either https://satijalab.org/seurat/v3.0/immune_alignment.html or https://satijalab.org/seurat/v3.0/pancreas_integration_label_transfer.html

immune.combined <- IntegrateData(anchorset = immune.anchors, dims = 1:20)

Merging dataset 1 into 2
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
Integrating data
Warning message:
“The new data doesn't have the same number of features as the current data”
Error: Attempting to add a different number of cells and/or features
Traceback:

1. IntegrateData(anchorset = immune.anchors, dims = 1:20)
2. SetAssayData(object = merged.obj, assay = assay, slot = "data", 
 .     new.data = integrated.matrix)
3. SetAssayData.Seurat(object = merged.obj, assay = assay, slot = "data", 
 .     new.data = integrated.matrix)
4. SetAssayData(object = object[[assay]], slot = slot, new.data = new.data)
5. SetAssayData.Assay(object = object[[assay]], slot = slot, new.data = new.data)
6. stop("Attempting to add a different number of cells and/or features", 
 .     call. = FALSE)

Any idea how can I solve the problem?

[fidelram]

I solved the problem by installing a commit from april 2:

devtools::install_github(repo = 'satijalab/seurat', ref = '8b9fe23ced436f34d4bb7d608b7f90f086edc33e', dependencies=FALSE, force=TRUE)

You may want to check what happened in between

[andrewwbutler]

This should now be resolved in the latest commit (as of cc45b311f4e0dc3b3c878356c6a555291bc614b3)

[RobertKSuter]

I've run into this same problem today. Integrating two objects worked fine, including a third is giving me the identical error to yours.

The new data doesn't have the same number of features as the current dataError: Attempting to add a different number of cells and/or features

Following new SCT integration vignette:

for (i in 1:length(Recurrent_int.list)) {
Recurrent_int.list[[i]] <- SCTransform(Recurrent_int.list[[i]], verbose = FALSE)
}

Recurrent_int.features <- SelectIntegrationFeatures(
object.list = Recurrent_int.list,
nfeatures = 3000

Recurrent_int.list <- PrepSCTIntegration(
object.list = Recurrent_int.list,
anchor.features = Recurrent_int.features,
verbose = FALSE)

Recurrent_int.anchors <- FindIntegrationAnchors(
object.list = Recurrent_int.list,
normalization.method = "SCT",
anchor.features = Recurrent_int.features,
verbose = FALSE
)

to_integrate <- Reduce(intersect, lapply([email protected], rownames))

Recurrent_int <- IntegrateData(
anchorset = Recurrent_int.anchors,
normalization.method = "SCT",
verbose = TRUE
)