title: Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data.
abstract: BACKGROUND
  Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cDNA. We employed our hyperspectral microarray scanner coupled with multivariate data analysis algorithms that independently identify and quantitate emissions from all sources to investigate three artifacts that reduce the accuracy and reliability of microarray data: skew toward the green channel, dye separation, and variable background emissions.
  
  
  RESULTS
  Here we demonstrate that several common microarray artifacts resulted from the presence of emission sources other than the labeled cDNA that can dramatically alter the accuracy and reliability of the array data. The microarrays utilized in this study were representative of a wide cross-section of the microarrays currently employed in genomic research. These findings reinforce the need for careful attention to detail to recognize and subsequently eliminate or quantify the presence of extraneous emissions in microarray images.
  
  
  CONCLUSIONS
  Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.
authors.affiliation: Sandia National Laboratories, Albuquerque, NM 87185, USA. jatimli@sandia.gov
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Timlin
authors.forename: David M
authors.initials: DM
authors.lastname: Haaland
authors.forename: Michael B
authors.initials: MB
authors.lastname: Sinclair
authors.forename: Anthony D
authors.initials: AD
authors.lastname: Aragon
authors.forename: M Juanita
authors.initials: MJ
authors.lastname: Martinez
authors.forename: Margaret
authors.initials: M
authors.lastname: Werner-Washburne
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000378:metabolism; D005456:Fluorescent Dyes / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D005800:Genes, Fungal; D023281:Genomics / Q000379:methods*; D008856:Microscopy, Fluorescence; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012984:Software
chemical_list: D018076:DNA, Complementary; D005456:Fluorescent Dyes