Harshlight: a "corrective make-up" program for microarray chips

Background: 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. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects. Results: We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. Conclusion: We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Mayte Suárez-Fariñas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco
• Keywords: BMCBI 2005, Chip, Image, Starkest Blemishes