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Significant Gene Selection Using Integrated Microarray Data Set with Batch Effect

Authors
 Kim Ki-Yeol  ;  Chung Hyun-Cheol  ;  Jeung Hei-Cheul  ;  Shin Ji-Hye  ;  Kim Tae-Soo  ;  Rha Sun-Young 
Citation
 Genomics & Informatics, Vol.4(3) : 110-117, 2006 
Journal Title
 Genomics & Informatics 
ISSN
 1598-866X 
Issue Date
2006
Abstract
In microarray technology, many diverse experimental features can cause biases including RNA sources, microarray production or different platforms, diverse sample processing and various experiment protocols. These systematic effects cause a substantial obstacle in the analysis of microarray data. When such data sets derived from different experimental processes were used, the analysis result was almost inconsistent and it is not reliable. Therefore, one of the most pressing challenges in the microarray field is how to combine data that comes from two different groups. As the novel trial to integrate two data sets with batch effect, we simply applied standardization to microarray data before the significant gene selection. In the gene selection step, we used new defined measure that considers the distance between a gene and an ideal gene as well as the between-slide and within-slide variations. Also we discussed the association of biological functions and different expression patterns in selected discriminative gene set. As a result, we could confirm that batch effect was minimized by standardization and the selected genes from the standardized data included various expression pattems and the significant biological functions.
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Appears in Collections:
1. Journal Papers (연구논문) > 1. College of Medicine (의과대학) > Medical Research Center (임상의학연구센터)
1. Journal Papers (연구논문) > 5. Research Institutes (연구소) > Cancer Metastasis Research Center (암전이연구센터)
1. Journal Papers (연구논문) > 5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소)
1. Journal Papers (연구논문) > 1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실)
Yonsei Authors
김기열(Kim, Ki Yeol) ORCID logo https://orcid.org/0000-0001-5357-1067
라선영(Rha, Sun Young)
신지혜(Shin, Ji Hye)
정현철(Chung, Hyun Cheol) ORCID logo https://orcid.org/0000-0002-0920-9471
정희철(Jeung, Hei Cheul)
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/110381
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