Hi everyone I have two questions: When can we use merge for Seurat objects? When can we use integration for Seurat objects? I have two datasets from different experiments. each dataset has cancer samples and healthy samples. To do clustering, I did the following: 1- I created a Seurat object for each sample, then I calculated QC and filtered the cell. 2- normalized each object with SCT 3- combined samples from each experiment together using merge() and then I made a list of two objects (two experiments) 4- applied reference-based integration to combine the two datasets. I used two samples (cancer and health) with high cell number from each dataset as a reference dataset. 4- Run PCA, UMAP, Find Neighbour, FindCluster.
This workflow worked, however, I am unsure if what I have done correctly in biology?
For one dataset with many samples, Could I apply the Seurat integration workflow instead of merge()?