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Merge seurat list

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
merge
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updated by GenoMax GenoMax • written by Long • Long

1 answer

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")
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written by bk11 • bk11

it worked! thanks!

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written by Long • Long

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer. enter image description here

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written by bk11 • bk11

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