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Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA?

scData <- scData %>% 
    RunUMAP(reduction = "harmony", dims = 1:14) %>% 
    FindNeighbors(reduction = "harmony", dims = 1:14) %>% 
    FindClusters(resolution = 0.2) %>% 
    identity()
numPC = 14
scData <- FindNeighbors(scData, dims = 1:numPC)
scData <- FindClusters(scData, resolution = 0.2, dims = 1:numPC)
scData <- RunUMAP(scData, dims = 1:numPC)

Both options give me different results. Not sure what the correct way to it is.


From the Broad Institute website: https://portals.broadinstitute.org/harmony/

"Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq."

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