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.

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