batch effcts and data integration

bioFAM / MOFA2

Multi-Omics Factor Analysis

https://biofam.github.io/MOFA2/

GNU Lesser General Public License v3.0

305 stars 52 forks source link

batch effcts and data integration #107

Closed wangjiawen2013 closed 1 year ago

wangjiawen2013 commented 2 years ago

Hi, There are various tools to perfrom batch effects removal or data integration in scRNAseq, such as CCA (seurat), scvi-tools, harmony, scanorama and so on. Can I use mofa/mofa2 for this purpose ? Is mofa/mofa2 an equivalence of these tools ?

rargelaguet commented 1 year ago

Hi @wangjiawen2013 , sorry for my very late reply, but MOFA should not be used for batch effect correction (i.e. horizontal data integration). The methods you mention are much better suited for this task. MOFA is a vertical integration method that is applicable when you have multi-omics from individual samples (or cells).

Maybe our review on single-cell data integration clarifies some of this concepts: https://www.nature.com/articles/s41587-021-00895-7