title: Detecting artifacts on SNP chips.
abstract: Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. We developed a tool, Harshlight, for the detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify defects. We demonstrate that Harshlight can be widely used for chips with different technologies thanks to its user-tunable parameters. Here we report its application to SNP microarrays.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Pellegrino
authors.forename: Mayte
authors.initials: M
authors.lastname: Suárez-Fariñas
authors.forename: Marcelo O
authors.initials: MO
authors.lastname: Magnasco
authors.forename: Knut M
authors.initials: KM
authors.lastname: Wittkowski
mesh_terms: D016477:Artifacts; D007091:Image Processing, Computer-Assisted; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results