Integrating data Error: Cannot add more or fewer cell meta.data information without values being named with cell names

Question

[aimanbarki]

I am trying to integrate after using SCT transform and receiving the following error:

Integrating data
Error: Cannot add more or fewer cell meta.data information without values being named with cell names

obj.list <- SplitObject(merged_seurat_filtered, split.by = 'orig.ident')
for(i in 1:length(obj.list)){
  obj.list[[i]] <- NormalizeData(object = obj.list[[i]])
  obj.list[[i]] <- FindVariableFeatures(object = obj.list[[i]])
}

# select integration features
features <- SelectIntegrationFeatures(object.list = obj.list)

# find integration anchors (CCA)
anchors <- FindIntegrationAnchors(object.list = obj.list,
                                  anchor.features = features)

# integrate data
seurat.integrated <- IntegrateData(anchorset = anchors)

# Scale data, run PCA and UMAP and visualize integrated data
seurat.integrated <- ScaleData(object = seurat.integrated)
seurat.integrated <- RunPCA(object = seurat.integrated)
seurat.integrated <- RunUMAP(object = seurat.integrated, dims = 1:20)
seurat.integrated <- RunTSNE(object = seurat.integrated, dims = 1:20)

Can someone explain the error? Why I am getting this? What I need to do?

[kevin.stachelek]

I am not sure what is causing this error. I think that the seurat github issues page would be lead to a quicker answer, though.

Answer 1

[aimanbarki]

Little background: I was using 6 human heart sc-RNA samples. I was trying to figure out how should I integrate my samples. I try using the following workflow:

1. First Workflow: normalized, scaled the all 6 objects and merged them
2. 2nd Workflow: normalized, scaled the all 6 objects and integrate them
3. 3rd Workflow: I was using the 1st workflow merged object and using it to SCTransform and integration.

       I did that in 3rd workflow because I when we run the SCTrasnsform it created the new assay. So i thought the previous normalization will not effect it. But it is not the case. 
   

   I don't under why but I received the error(mention in question) when I try 3rd workflow and I able to get rid of the error if I simply avoid normalization and scaling at first place