Integration of SCTransform normalized seurat object

[w-julie]

Hi all,

I have three dataset that have been normalized separately using SCTransform. I now want to integrate them and to do so I follow the Seurat vignette with running in this order the functions:

• SelectIntegrationFeatures
• PrepSCTIntegration
• FindIntegrationAnchors
• IntegrateData When I run the IntegrateData I have the following error message, but I cannot understand what it means. Do anyone else already have this issue ?

"Merging dataset 3 into 1 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Integrating data Error in x$.self$finalize() : attempt to apply non-function Merging dataset 2 into 1 3 Error in RowMergeMatricesList(mat_list = all.mat, mat_rownames = all.rownames, : std::bad_alloc"

Thank you for your help !

[f6v]

Could be that you're running low on RAM.

[saketkc]

Hi @w-julie, this does appear to be a memory issue. How many cells do you have in your dataset and how much RAM does the system have?

[saketkc]

Closing due to inactivity.