I have 3 patients with normal and tumor tissue sample(10× technology), there are six samples in total. I want combine them and find whether there is some difference between normal and tumor sample in specific cell type (such as immune cell). Due to different patients, it may have batch effect. I am struggle to choose integrate method.
My question is that:
For the Seurat integrate method, SCtransform method, harmony method, which one is more suitable for my case, or I just merge six sample together directly?
If use Seurat integrate pipeline and SCtransform pipeline, they recommand to use "RNA" assay instead of "integrate" assay to do Findmarker, for my understanding, "RNA" assay is batch-uncorrect matrix, will it cause some problem? Or there are other better options to do it?
Thanks a lot, hope to get your suggestions!