a probe-treatment-reference (ptr) model for the analysis of oligonucleotide expression microarraysprobe-treatment-reference(ptr)模型分析寡核苷酸微阵列表达.pdfVIP

BMC Bioinformatics BioMed Central Methodology article Open Access A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays 1 1 1,2 Huanying Ge , Chao Cheng and Lei M Li* Address: 1Molecular and Computational Biology, Department of Biology Sciences, University of Southern California, Los Angeles, CA 90089- 2910, USA and 2Department of Mathematics, University of Southern California, Los Angeles, CA 90089-2910, USA Email: Huanying Ge - hge@; Chao Cheng - chaochen@; Lei M Li* - lilei@ * Corresponding author Published: 14 April 2008 Received: 6 June 2007 Accepted: 14 April 2008 BMC Bioinformatics 2008, 9:194 doi:10.1186/1471-2105-9-194 This article is available from: /1471-2105/9/194 © 2008 Ge et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Microarray pre-processing usually consists of normalization and summarization. Normalization aims to remove non-biological variations across different arrays. The normalization algorithms generally require the specification of reference and target arrays. The issue of reference selection has not been fully addressed. Summarization aims to estimate the transcript abundance from normalized