Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples 英文参考文献.docVIP

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Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples 英文参考文献.doc

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Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples 英文参考文献

EvaluationofMicroarrayPreprocessingAlgorithms BasedonConcordancewithRT-PCRinClinicalSamples BalazsGyorffy1,BelaMolnar1,HermannLage2,ZoltanSzallasi3,4,AronC.Eklund3,4 * 1HungarianAcademyofSciencesandSemmelweisUniversityBudapest,Budapest,Hungary,2Charite′Universita¨tsmedizinBerlin,InstituteofPathology,Berlin,Germany, 3Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark, 4Children’s Hospital Boston, Boston, Massachusetts, United States of America Abstract Background:SeveralpreprocessingalgorithmsforAffymetrixgeneexpressionmicroarrayshavebeendeveloped,andtheir performanceonspike-indatasetshasbeenevaluatedpreviously.However,acomprehensivecomparisonofpreprocessing algorithmsonsamplestakenunderresearchconditionshasnotbeenperformed. Methodology/Principal Findings: We used TaqMan RT-PCR arrays as a reference to evaluate the accuracy of expression valuesfromAffymetrixmicroarraysintwoexperimentaldatasets:onecomprising84genesin36colonbiopsies,andthe other comprising 75 genes in 29 cancer cell lines. We evaluated consistency using the Pearson correlation between measurementsobtainedonthetwoplatforms.Also,weintroducethelog-ratiodiscrepancyasamorerelevantmeasureof discordancebetweengeneexpressionplatforms.Ofninepreprocessingalgorithmstested,PLIER+16producedexpression valuesthatweremostconsistentwithRT-PCRmeasurements,althoughthedifferenceinperformancebetweenmostofthe algorithmswasnotstatisticallysignificant. Conclusions/Significance:OurresultssupportthechoiceofPLIER+16forthepreprocessingofclinicalAffymetrixmicroarray data.However,otheralgorithmsperformedsimilarlyandareprobablyalsogoodchoices. Citation: Gyorffy B,Molnar B, LageH, SzallasiZ,EklundAC (2009) Evaluation ofMicroarray PreprocessingAlgorithms BasedonConcordance withRT-PCR in ClinicalSamples.PLoSONE4(5):e5645.doi:10.1371/journal.pone.0005645 Editor:ChadCreighton,BaylorCollegeofMedicine,UnitedStatesofAmerica ReceivedMarch15,2009;AcceptedApril24,2009;PublishedMay21,2009 Copyright: ? 2