Question: Finding Subclusters in Seurat Clusters
gravatar for fouerghi20
5 weeks ago by
fouerghi2020 wrote:

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.

ADD COMMENTlink modified 5 weeks ago by jared.andrews077.9k • written 5 weeks ago by fouerghi2020
gravatar for jared.andrews07
5 weeks ago by
Memphis, TN
jared.andrews077.9k wrote:

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.

ADD COMMENTlink written 5 weeks ago by jared.andrews077.9k

Thank you Andrew. I appreciate the help.

ADD REPLYlink written 28 days ago by fouerghi2020
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