Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/5230
Title: Summarization methods and quality problems in Affymetrix microarrays
Contributor(s): Gondro, Cedric  (author)orcid 
Publication Date: 2009
Handle Link: https://hdl.handle.net/1959.11/5230
Abstract: The quality of RNA samples and slide hybridizations are paramount for gene expression studies. Here the focus is on hybridization quality in Affymetrix arrays and a comparison of the results of differential expression analysis for six summarization methods using slides of good and bad quality. The overlap of probes detected as differentially expressed across methods is very small even with good arrays. Slides of inferior quality also significantly change the generated list of differentially expressed genes. Extensive qualitative and quantitative quality control measures should be used prior to downstream analyses of data to ensure early detection and removal of problematic slides. Given the high variability of results across summarization methods it is recommended that different methods are used to conduct analyses and the intersecting results of these are used for further downstream analyses.
Publication Type: Conference Publication
Conference Details: AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 27th September - 1st October, 2009
Source of Publication: Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.18, p. 304-307
Publisher: Association for the Advancement of Animal Breeding and Genetics (AAABG)
Place of Publication: Armidale, Australia
ISSN: 1328-3227
Fields of Research (FoR) 2008: 010402 Biostatistics
060405 Gene Expression (incl Microarray and other genome-wide approaches)
Socio-Economic Objective (SEO) 2008: 970106 Expanding Knowledge in the Biological Sciences
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Publisher/associated links: http://trove.nla.gov.au/work/36420775
http://www.aaabg.org/proceedings18/files/gondro304.pdf
http://aaabg.org/aaabg18/
Appears in Collections:Conference Publication
School of Environmental and Rural Science

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