A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies.

ABSTRACT: Genome projects now generate large-scale data often produced at various time points by different laboratories using multiple platforms. This increases the potential for batch effects. Currently there are several batch evaluation methods like principal component analysis (PCA; mostly based on visual inspection), and sometimes they fail to reveal all of the underlying batch effects. These methods can also lead to the risk of unintentionally correcting biologically interesting factors attributed to batch effects. Here we propose a novel statistical method, finding batch effect (findBATCH), to evaluate batch effect based on probabilistic principal component and covariates analysis (PPCCA). The same framework also provides a new approach to batch correction, correcting batch effect (correctBATC

SUBMITTER: Nyamundanda G 

PROVIDER: S-EPMC5589920 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature