Detecting artifacts on SNP chips

Author

Pellegrino, M. ; Suarez-Farinas, M. ; Magnasco, M.O. ; Wittkowski, K.M.

fYear

2006

fDate

Aug. 30 2006-Sept. 3 2006

Firstpage

4100

Lastpage

4102

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

Keywords

biochemistry; biological techniques; fluorescence; genetics; image processing; molecular biophysics; statistical analysis; HDONA microarray chips; artifacts detection; fluorescence image; glass flaws; high-density oligonucleotide arrays; image processing method; microarray scans; single nucleotide polymorphism microarray chips; statistics method; surface coatings; uneven fluid distribution; user-tunable parameters; Bioinformatics; Cities and towns; Fluorescence; Gene expression; Genomics; Humans; Image processing; Microscopy; Probes; USA Councils;

fLanguage

English

Publisher

ieee

Conference_Titel

Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE

Conference_Location

New York, NY

ISSN

1557-170X

Print_ISBN

1-4244-0032-5

Electronic_ISBN

1557-170X

Type

conf

DOI

10.1109/IEMBS.2006.260753

Filename

4462702