TAILIEUCHUNG - Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

Tham khảo tài liệu 'normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships', tài chính - ngân hàng, kế toán - kiểm toán phục vụ nhu cầu học tập, nghiên cứu và làm việc hiệu quả | Method Open Access Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships Alan R Dabney and John D StoreyỶ Addresses Department of Statistics Texas A M University College Station TX 77843 USA. Department of Biostatistics and Department of Genome Sciences University of Washington WA 98195 USA. Correspondence John D Storey. Email jstorey@ Published 28 March 2007 Genome Biology 2007 8 R44 doi 186 gb-2007-8-3-r44 The electronic version of this article is the complete one and can be found online at http 2007 8 3 R44 Received 30 October 2006 Revised 5 February 2007 Accepted 28 March 2007 2007 Dabney and Storey licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract In normalizing two-channel expression arrays the ANOVA approach explicitly incorporates the experimental design in its model and the MA plot-based approach accounts for intensitydependent biases. However both approaches can lead to inaccurate normalization in fairly common scenarios. We propose a method called efficient Common Array Dye Swap eCADS for normalizing two-channel microarrays that accounts for both experimental design and intensitydependent biases. Under reasonable experimental designs eCADS preserves differential expression relationships and requires only a single array per sample pair. Background The two-channel microarray continues to be an important platform for characterizing genomewide expression levels. For example a two-channel array technology using inkjet printing techniques was recently introduced by Agilent Laboratories Palo Alto California that combines some of the favorable properties of single-channel oligonucleotide arrays and two-channel cDNA .

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