Integrating data Error: Cannot add more or fewer cell meta.data information without values being named with cell names
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0
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3 months ago
aimanbarki ▴ 20

I am trying to integrate after using SCT transform and reciecing 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?

data Error SCTransform Integration • 616 views
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1
Entering edit mode

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.

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0
Entering edit mode
3 months ago
aimanbarki ▴ 20

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
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