Transformation, normalization and batch effect in the analysis of mass   spectrometry data for omics studies
  Data transformation, normalization and handling of batch effect are a key part of data analysis for almost all spectrometry-based omics data. This paper reviews and contrasts these three distinct aspects. We present a systematic overview of the key approaches and critically review some common procedures. Much of this paper is inspired by mass spectrometry based experimentation, but most of our discussion carries over to omics data using distinct spectrometric approaches generally. 
Bart J. A. Mertens
stat.ME