Finding Subclusters in Seurat Clusters
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12 months ago
fouerghi20 ▴ 50

I have performed clustering on my Seurat object and I would like to focus on one specific cluster and find study its subclusters. To do this, I understand that you have to subset the Seurat object. However, do I also have to run FindVariableFeatures() on this subset and then RunPCA again to find the appropriate dimensions to proceed with dimensionality reduction? I ran it with both this and without it and it yielded quite different results. Not sure which process is correct. Any help is appreciated.

seurat scRNAseq cluster subcluster • 2.3k views
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12 months ago

Yes, you will want to re-run those steps. The variable features within that cluster and between all the others are likely very different, which will have dramatic effects on the dimensionality reduction. Without doing so, I expect it'll struggle to pull out many meaningful sub-clusters.

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Thank you Andrew. I appreciate the help.

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Hi Andrew, Do we still have to run NormalizeData and ScaleData, as well as FindVariableFeatures and RunPCA?

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You shouldn't have to run NormalizeData again since it's just doing a log transformation and multiplying by a scaling factor, but the others, yes.

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Thank you!

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