cKBET:assessing goodness of batch effect correction for single-cell RNA-seq  

作　　者：Yameng ZHAO Yin GUO Limin LI 

机构地区：[1]School of Mathematics and Statistics,Xi’an Jiaotong University,Xi’an 710049,China

出　　处：《Frontiers of Computer Science》2024年第1期215-228,共14页中国计算机科学前沿（英文版）

基　　金：supported by the NSFC projects(Grant No.11631012).

摘　　要：Single-cell RNA sequencing reveals the gene structure and gene expression status of a single cell,which can reflect the heterogeneity between cells.However,batch effects caused by non-biological factors may hinder data integration and downstream analysis.Although the batch effect can be evaluated by visualizing the data,which actually is subjective and inaccurate.In this work,we propose a quantitative method cKBET,which considers the batch and cell type information simultaneously.The cKBET method accesses batch effects by comparing the global and local fraction of cells of different batches in different cell types.We verify the performance of our cKBET method on simulated and real biological data sets.The experimental results show that our cKBET method is superior to existing methods in most cases.In general,our cKBET method can detect batch effect with either balanced or unbalanced cell types,and thus evaluate batch correction methods.

关 键 词：single-cell RNA-seq dataset b batch effect assessment cKBET method 

分 类 号：TP274[自动化与计算机技术—检测技术与自动化装置] Q811.4[自动化与计算机技术—控制科学与工程]