title: Microarray image segmentation using additional dye--an experimental study.
abstract: The DNA microarray technique allows monitoring the expression levels of thousands of genes simultaneously. A single DNA microarray experiment involves a number of error-prone manual and automated processes, which influence the results and have an impact on the subsequent stages of analysis. Typical problems of arrays are pinning errors while probe printing and the corruption of spots by noise patches. These errors should be detected at the time of image analysis in order to prevent the erroneous intensities from ending up in the analysis and inference stages.
  
  
  RESULTS
  In this paper we introduce the concept (referred to as SybrSpot) of utilizing information provided by an additional dye, SYBR green RNA II, for segmentation of gene expression microarrays. Owing to the effective binding of the SYBR green RNA II to the array probes, an image with high signal-to-noise ratio is obtained. This image is used to learn about the spot quality and to flag spots which are not reliably hybridized and corrupted by noise. Further, we compare SybrSpot with GenePix and demonstrate that SybrSpot performs better than GenePix when flagging spots with no probes or weak probes.
  
  
  BACKGROUND
  The code is available upon request to authors.
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland. rashi.gupta@helsinki.fi
authors.forename: Rashi
authors.initials: R
authors.lastname: Gupta
authors.forename: Salla
authors.initials: S
authors.lastname: Ruosaari
authors.forename: Sangita
authors.initials: S
authors.lastname: Kulathinal
authors.forename: Jaakko
authors.initials: J
authors.lastname: Hollmén
authors.forename: Petri
authors.initials: P
authors.lastname: Auvinen
mesh_terms: D002460:Cell Line; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009930:Organic Chemicals / Q000378:metabolism*
chemical_list: D009930:Organic Chemicals; C098798:SYBR Green II