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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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RNA assay in seurat object for hdWGCNA, should I remove integrated assay? #9287

Closed yulchen810 closed 2 months ago

yulchen810 commented 2 months ago

Hi, I have a seurat object containing 6 samples(seurat v4), I performed integration to correct batch effect-following https://satijalab.org/seurat/articles/integration_introduction.html. Now I have two assays: "RNA" and "integrated".

I want to use this seurat object to do hdWGCNA analysis.

  1. Should I use "RNA" assay? Because I tried to use "integrated" assay, an error occur when SetupForWGCNA, and it worked when I use "RNA" assay.
  2. Should I remove "integrated" assay? I tried to do MetacellsByGroups after the fisrt step in 1, it return me an ERROR again, Error in MetacellsByGroups(seurat_obj = seurat_obj, group.by = c("cell_type", : Invalid reduction (harmony). Reductions in Seurat object: pca, umap

The structure of my seurat object is like below: image

The data in "RNA" assay only be normalized, so I need to perform ScaleData, PCA and UMAP to "RNA" assay, and use the result to do hdWGCNA, right? If then, do I need to remove integrated assay from seurat object or I just keep it which will not affect hdWGCNA analysis?

Thank you very much! Best

samuel-marsh commented 2 months ago

Hi,

Not member of dev team but hopefully can be helpful. As this question is on best practices running hdWGCNA I would suggest posting to the GitHub repo for that package to hear from devs on best way to proceed.

Best, Sam

yulchen810 commented 2 months ago

@samuel-marsh I have already posted this question on hdWGCNA repo. Thank you!