5.3.4 Seurat两种数据比较：integrated vs RNA assay

刘小泽写于2020.11.16

内容来自：https://www.biostars.org/p/399789/

主要探讨多个数据利用Seurat整合后，会出现integrated 和 RNA assay

那么它们的区别在哪里呢？

Q1：What is this integrated assay and how/why is it different than "RNA".

• This is the data after integration. You can think of it as batch-adjusted data. 也就是说integrated assay是校正完批次效应后的数据

• data integration process will return a matrix with "corrected" value. Set DefaultAssay to "integrated" means your following analysis will on the "corrected" value.

• Set DefaultAssay to "RNA" means your following analysis will on the original value.

• You can use integrated data to do clustering. But it is not proper to use integrated for DE, and most tools only accept raw counts for DE.

Q2：What are the consequences of NOT changing it and leaving RNA as the default

• If you do not switch to integrated assay, you will not be working with integrated data.

• If you are not interested in the integrated data, then you don't need to perform integration. If you just want to combine two Seurat objects without any additional adjustments, there a merge function and a vignette for that workflow.