Figure 2
From: A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies
Detection of batch effect in pooled breast cancer gene expression datasets. (A) A PCA plot showing clustering of samples according to batches (three breast cancer datasets – GSE23593, GSE13787 and GSE12763). (B) BIC values from findBATCH showing the optimal number of pPCs for pooled/merged (three) datasets. The higher the BIC value, the better the model. The red dashed vertical line identifies the optimal number of pPCs. (C). A forest plot depicting different pPCs from findBATCH applied to quantify batch effect before correction.
