|Publication type:||Article in scientific journal|
|Type of review:||Peer review (publication)|
|Title:||Quality assessment of affymetrix GeneChip data|
|Published in:||OMICS: A Journal of Integrative Biology|
|Publisher / Ed. Institution:||Liebert|
|Subject (DDC):||570: Biology|
|Abstract:||Affymetrix GeneChips are one of the best established microarray platforms. This powerful technique allows users to measure the expression of thousands of genes simultaneously. However, a microarray experiment is a sophisticated and time consuming endeavor with many potential sources of unwanted variation that could compromise the results if left uncontrolled. Increasing data volume and data complexity have triggered growing concern and awareness of the importance of assessing the quality of generated microarray data. In this review, we give an overview of current methods and software tools for quality assessment of Affymetrix GeneChip data. We focus on quality metrics, diagnostic plots, probe-level methods, pseudo-images, and classification methods to identify corrupted chips. We also describe RNA quality assessment methods which play an important role in challenging RNA sources like formalin embedded biopsies, laser-micro dissected samples, or single cells. No wet-lab methods are discussed in this paper.|
|Fulltext version:||Published version|
|License (according to publishing contract):||Licence according to publishing contract|
|Departement:||School of Engineering|
|Organisational Unit:||Institute of Data Analysis and Process Design (IDP)|
|Appears in Collections:||Publikationen School of Engineering|
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