Assessment of Batch Normalization Methods on Mass Cytometry Data

Poster Highlights

• In this study, we used 68 PBMC samples from melanoma patients to assess the effectiveness of two batch normalization tools, CytoNorm and cyCombine.
• We found that both methods preserved biological variance, through the evaluation of their MAD scores.
• CyCombine demonstrated superior performance in reducing technical variation with an Earth Mover's Distance reduction of 0.70, compared to CytoNorm's 0.37.
• The findings highlight the complexity of removing batch variation without distorting true biological signals, emphasizing the need for careful selection of normalization methods in multi-batch experiments.