Merge seurat list

Question

[Long]

Good morning,

I have a question about how to merge Seurat objects. My Seurat objects are from separately integrated datasets using Harmony. The reason for performing separate Harmony integration is that the data size is too large and cannot be integrated effectively as a single dataset. Now, I want to merge these objects together. However, I have encountered a failure, and my error message is:

testMerge <- merge(othercell, y = tcell, project = "TestMerge")
Error in apply(X = GetAssayData(object = object, assay = assay, slot = "scale.data")[,  : 
  dim(X) must have a positive length

Answer 1

[bk11]

Most probably your data might have been integrated data w/ SCT performed. Can you try setting the SCT assay to NULL and see if merge works?

othercell[['SCT']] <- NULL
tcell[['SCT']] <- NULL
testMerge <- merge(x=othercell, y = tcell, project="TestMerge")

[Long]

it worked! thanks!

[bk11]

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