"Harshlighting" small blemishes on microarrays

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 show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs). Results: We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion: Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method pro...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Mayte Suárez-Fariñas, Asifa Haider, Knut M. Wittkowski
• Keywords: BMCBI 2005, Image, Subtle Expression Changes, Uneven Distribution