title: Advanced spot quality analysis in two-colour microarray experiments.
abstract: BACKGROUND
  Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information.
  
  
  RESULTS
  We evaluated the performance of two image analysis packages MAIA and GenePix (GP) using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5%) than GP with default spot filtering conditions.
  
  
  CONCLUSIONS
  Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.
authors.affiliation: Microarray Center/LBMAGM, CRP-Santé, 84 Rue Val Fleuri, L-1526, Luxembourg. mikalai.yatskou@uni.lu
authors.forename: Mikalai
authors.initials: M
authors.lastname: Yatskou
authors.forename: Eugene
authors.initials: E
authors.lastname: Novikov
authors.forename: Guillaume
authors.initials: G
authors.lastname: Vetter
authors.forename: Arnaud
authors.initials: A
authors.lastname: Muller
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
authors.forename: Laurent
authors.initials: L
authors.lastname: Vallar
authors.forename: Evelyne
authors.initials: E
authors.lastname: Friederich
references.citation: Nat Rev Cancer. 2007 Jun;7(6):415-28
references.pmid: 17508028
references.citation: Genome Biol. 2003;4(1):R5
references.pmid: 12540297
references.citation: Bioinformatics. 2005 Sep 1;21(17):3578-9
references.pmid: 16046497
references.citation: Cancer Res. 2005 Jul 15;65(14):6237-44
references.pmid: 16024625
references.citation: Genomics. 2002 Oct;80(4):385-94
references.pmid: 12376092
references.citation: Nat Rev Genet. 2006 Mar;7(3):200-10
references.pmid: 16485019
references.citation: BMC Bioinformatics. 2006 Jul 06;7:335
references.pmid: 16824223
references.citation: Nat Cell Biol. 2000 Feb;2(2):76-83
references.pmid: 10655586
references.citation: J Biol Chem. 2005 Mar 25;280(12):11740-8
references.pmid: 15647282
references.citation: BMC Genomics. 2007 Aug 29;8:294
references.pmid: 17727702
references.citation: Bioinformatics. 2006 Oct 15;22(20):2554-5
references.pmid: 16899490
references.citation: Nat Biotechnol. 2006 Sep;24(9):1151-61
references.pmid: 16964229
references.citation: J Bioinform Comput Biol. 2005 Dec;3(6):1411-28
references.pmid: 16374914
references.citation: J Biopharm Stat. 2007;17(3):415-31
references.pmid: 17479391
references.citation: Genes Dev. 2004 May 15;18(10):1131-43
references.pmid: 15155580
references.citation: Nucleic Acids Res. 2001 Aug 1;29(15):E75-5
references.pmid: 11470890
references.citation: BMC Bioinformatics. 2005 Dec 09;6:293
references.pmid: 16336688
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D766-70
references.pmid: 17182626
references.citation: Biotechniques. 2003 Feb;34(2):374-8
references.pmid: 12613259
references.citation: Nat Genet. 2005 Feb;37(2):182-6
references.pmid: 15640797
references.citation: Nucleic Acids Res. 2002 Jun 15;30(12):e54
references.pmid: 12060692
references.citation: Bioinformatics. 2007 Mar 1;23(5):639-40
references.pmid: 17237062
references.citation: BMC Bioinformatics. 2006 Jun 16;7:306
references.pmid: 16780582
references.citation: Appl Bioinformatics. 2006;5(4):255-66
references.pmid: 17140272
references.citation: Nat Med. 2004 Sep;10(9):917-9
references.pmid: 15322538
references.citation: Bioinformatics. 2005 Apr 15;21(8):1572-8
references.pmid: 15615693
references.citation: BMC Bioinformatics. 2005 Jul 05;6:168
references.pmid: 15998470