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

> 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

![](https://1260378310-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MCv4XZpjUYDdSrsYVkw%2F-MN2OiutUio80lq_NCBd%2F-MN2P9NH8JafvVbZU0Sz%2Fimage.png?alt=media\&token=8538375f-24f8-43ea-8148-c5b2681d4e63)

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.&#x20;
* 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.&#x20;
* 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](https://satijalab.org/seurat/v3.1/merge_vignette.html).