Gridding the spot centers of microarray images

Jinn Ho; Wen Liang Hwang; Henry Horn Shing Lu; D. T. Lee

Gridding the spot centers of microarray images

Jinn Ho^*, Wen Liang Hwang, Henry Horn Shing Lu, D. T. Lee

^*Corresponding author for this work

Institute of Statistics

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

Abstract

We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images. We compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically.

Original language	English
Title of host publication	13th European Signal Processing Conference, EUSIPCO 2005
Pages	596-599
Number of pages	4
State	Published - Sep 2005
Event	13th European Signal Processing Conference, EUSIPCO 2005 - Antalya, Turkey Duration: 4 Sep 2005 → 8 Sep 2005

Publication series

Name	13th European Signal Processing Conference, EUSIPCO 2005

Conference

Conference	13th European Signal Processing Conference, EUSIPCO 2005
Country/Territory	Turkey
City	Antalya
Period	4/09/05 → 8/09/05

Cite this

@inproceedings{bc736072faa94747b9694c0e6ccaac08,

title = "Gridding the spot centers of microarray images",

abstract = "We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images. We compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically.",

author = "Jinn Ho and Hwang, {Wen Liang} and Lu, {Henry Horn Shing} and Lee, {D. T.}",

year = "2005",

month = sep,

language = "English",

isbn = "1604238216",

series = "13th European Signal Processing Conference, EUSIPCO 2005",

pages = "596--599",

booktitle = "13th European Signal Processing Conference, EUSIPCO 2005",

note = "13th European Signal Processing Conference, EUSIPCO 2005 ; Conference date: 04-09-2005 Through 08-09-2005",

}

TY - GEN

T1 - Gridding the spot centers of microarray images

AU - Ho, Jinn

AU - Hwang, Wen Liang

AU - Lu, Henry Horn Shing

AU - Lee, D. T.

PY - 2005/9

Y1 - 2005/9

N2 - We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images. We compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically.

AB - We use an optimization technique to accurately locate a distorted grid structure in a microarray image. By assuming that spot centers deviate smoothly from a checkerboard grid structure, we show that the process of gridding spot centers can be formulated as a constrained optimization problem. The constraint is equal to the variations of the transform parameter. We demonstrate the accuracy of our algorithm on two sets of microarray images. One set consists of some images from the Stanford Microarray Database; we compare our centers with those annotated in the Database. The other set consists of oligonucleotide images. We compare our results with those obtained by GenePix Pro 5.0. Our experiments were performed completely automatically.

UR - http://www.scopus.com/inward/record.url?scp=84863650465&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84863650465

SN - 1604238216

SN - 9781604238211

T3 - 13th European Signal Processing Conference, EUSIPCO 2005

SP - 596

EP - 599

BT - 13th European Signal Processing Conference, EUSIPCO 2005

T2 - 13th European Signal Processing Conference, EUSIPCO 2005

Y2 - 4 September 2005 through 8 September 2005

ER -

Gridding the spot centers of microarray images

Abstract

Publication series

Conference

Other files and links

Fingerprint

Cite this