Title: Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays

Authors: Zhongxue Chen, Monnie McGee, Qingzhong Liu, Y. Megan Kong, Xudong Huang, Jack Y. Yang, Richard H. Scheuermann

Addresses: Biostatistics/Epidemiology/Research Design Core, Center for Clinical and Translational Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA. ' Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA. ' Department of Computer Science, Sam Houston State University, Huntsville, TX 77341, USA. ' Department of Pathology, University of Texas Southwestern Medical Center Dallas, TX 75390, USA. ' Conjugate and Medicinal Chemistry Laboratory, Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. ' Center for Research in Biological Systems, University of California at San Diego, La Jolla, CA 92093-0043, USA. ' Department of Pathology, University of Texas Southwestern Medical Center Dallas, TX 75390, USA

Abstract: We propose a new method based on probe-level data (PLIDEG) to filter differentially expressed genes from non-differentially expressed genes. We compare this new method with others based on expression values by using two spikein data sets. With the extra information provided by probe level data, PLIDEG not only controls type I error, but also increases the power of detecting DEGs, simultaneously. Therefore, PLIDEG can efficiently separate DEGs and non-DEGs without requiring the estimation of the number of non-DEGs. Based on theoretical analysis and results from application to real microarray data, we confirm these good features of this new method.

Keywords: microarray data; GnenChip arrays; FDR; false discovery rate; probe level data; preprocessing method; DEGs; differentially expressed genes; SAM; gene expression; gene selection.

DOI: 10.1504/IJCBDD.2010.038028

International Journal of Computational Biology and Drug Design, 2010 Vol.3 No.3, pp.237 - 257

Published online: 11 Jan 2011 *

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