Detecting artifacts on SNP chips

Maurizio Pellegrino; Mayte Suárez-Fariñas; Marcelo O. Magnasco; Knut M. Wittkowski

doi:10.1109/IEMBS.2006.260753

Detecting artifacts on SNP chips

Maurizio Pellegrino, Mayte Suárez-Fariñas, Marcelo O. Magnasco, Knut M. Wittkowski

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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.

Original language	English
Title of host publication	28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06
Pages	4100-4102
Number of pages	3
DOIs	https://doi.org/10.1109/IEMBS.2006.260753
State	Published - 2006
Event	28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06 - New York, NY, United States Duration: 30 Aug 2006 → 3 Sep 2006

Publication series

Name	Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
ISSN (Print)	0589-1019

Conference

Conference	28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06
Country/Territory	United States
City	New York, NY
Period	30/08/06 → 3/09/06

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10.1109/IEMBS.2006.260753

Cite this

Pellegrino, M., Suárez-Fariñas, M., Magnasco, M. O., & Wittkowski, K. M. (2006). Detecting artifacts on SNP chips. In 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06 (pp. 4100-4102). [4030446] (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings). https://doi.org/10.1109/IEMBS.2006.260753

@inproceedings{b42dcf6d5c2348a5b8436bcf5fa9dbdd,

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.",

author = "Maurizio Pellegrino and Mayte Su{\'a}rez-Fari{\~n}as and Magnasco, {Marcelo O.} and Wittkowski, {Knut M.}",

year = "2006",

doi = "10.1109/IEMBS.2006.260753",

language = "English",

isbn = "1424400325",

series = "Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings",

pages = "4100--4102",

booktitle = "28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06",

note = "28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06 ; Conference date: 30-08-2006 Through 03-09-2006",

}

Pellegrino, M, Suárez-Fariñas, M, Magnasco, MO & Wittkowski, KM 2006, Detecting artifacts on SNP chips. in 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06., 4030446, Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings, pp. 4100-4102, 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06, New York, NY, United States, 30/08/06. https://doi.org/10.1109/IEMBS.2006.260753

Detecting artifacts on SNP chips. / Pellegrino, Maurizio; Suárez-Fariñas, Mayte; Magnasco, Marcelo O. et al.
28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06. 2006. p. 4100-4102 4030446 (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Detecting artifacts on SNP chips

AU - Pellegrino, Maurizio

AU - Suárez-Fariñas, Mayte

AU - Magnasco, Marcelo O.

AU - Wittkowski, Knut M.

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

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U2 - 10.1109/IEMBS.2006.260753

DO - 10.1109/IEMBS.2006.260753

M3 - Conference contribution

C2 - 17947067

AN - SCOPUS:34047174156

SN - 1424400325

SN - 9781424400324

T3 - Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

SP - 4100

EP - 4102

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

T2 - 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06

Y2 - 30 August 2006 through 3 September 2006

ER -

Detecting artifacts on SNP chips

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