reproducible cancer biomarker discovery in seldi-tof ms using different pre-processing algorithms可再生的癌症生物标志物发现seldi-tof女士使用不同的预处理算法.pdfVIP

Reproducible Cancer Biomarker Discovery in SELDI-TOF MS Using Different Pre-Processing Algorithms 1 1 2 1 1 1 1,2 Jinfeng Zou , Guini Hong , Xinwu Guo , Lin Zhang , Chen Yao , Jing Wang , Zheng Guo * 1 Bioinformatics Centre, School of Life Science, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China, 2 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China Abstract Background: There has been much interest in differentiating diseased and normal samples using biomarkers derived from mass spectrometry (MS) studies. However, biomarker identification for specific diseases has been hindered by irreproducibility. Specifically, a peak profile extracted from a dataset for biomarker identification depends on a data pre- processing algorithm. Until now, no widely accepted agreement has been reached. Results: In this paper, we investigated the consistency of biomarker identification using differentially expressed (DE) peaks from peak profiles produced by three widely used average spectrum-dependent pre-processing algorithms based on SELDI- TOF MS data for prostate and breast cancers. Our results revealed two important factors that affect the consistency of DE peak identification using different algorithms. One factor is that some DE peaks selected from one peak profile were not detected as peaks in other profiles, and the second factor is that the statistical power of identifying DE peaks in large peak profiles with many peaks may be low due to the large scale of the tests and small number of samples. Furthermore, we demonstrated that the DE peak detection power in large prof