Journal de protéomique et bioinformatique
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Statistical Analysis of Protein Microarray Data: A Case Study in Type 1 Diabetes Research

Le TT An, Anna Pursiheimo, Robert Moulder and Laura L Elo

In this report we provide an overview of protein microarrays and devote particular consideration on the statistical methods used in data analysis with applications concerning the study of type 1 diabetes. The latter methodologies are illustrated with publically available data from a study that identified novel type 1 diabetes associated autoantibodies. Amongst the methods employed, Reproducibility-Optimized Test Statistic (ROTS) shows better detection over the widely used LIMMA. With the application of this analytical approach, we identify new protein biomarkers that were not previously reported in original investigation. This observation emphasises the benefit of using different methods to extract critical information in the analysis of microarray data.