I want to use this seurat object to do hdWGCNA analysis.
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.
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:
The data in "RNA" assay only be normalized, so I need to perform ScaleData, PCA, Harmony 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?
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.
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:
The data in "RNA" assay only be normalized, so I need to perform ScaleData, PCA, Harmony 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