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dc.contributor.authorShi, W
dc.contributor.authorOshlack, A
dc.contributor.authorSmyth, GK
dc.date.accessioned2020-12-18T03:28:13Z
dc.date.available2020-12-18T03:28:13Z
dc.date.issued2010-12-01
dc.identifierpii: gkq871
dc.identifier.citationShi, W., Oshlack, A. & Smyth, G. K. (2010). Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips. NUCLEIC ACIDS RESEARCH, 38 (22), https://doi.org/10.1093/nar/gkq871.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/11343/255783
dc.description.abstractFive strategies for pre-processing intensities from Illumina expression BeadChips are assessed from the point of view of precision and bias. The strategies include a popular variance stabilizing transformation and model-based background corrections that either use or ignore the control probes. Four calibration data sets are used to evaluate precision, bias and false discovery rate (FDR). The original algorithms are shown to have operating characteristics that are not easily comparable. Some tend to minimize noise while others minimize bias. Each original algorithm is shown to have an innate intensity offset, by which unlogged intensities are bounded away from zero, and the size of this offset determines its position on the noise-bias spectrum. By adding extra offsets, a continuum of related algorithms with different noise-bias trade-offs is generated, allowing direct comparison of the performance of the strategies on equivalent terms. Adding a positive offset is shown to decrease the FDR of each original algorithm. The potential of each strategy to generate an algorithm with an optimal noise-bias trade-off is explored by finding the offset that minimizes its FDR. The use of control probes as part of the background correction and normalization strategy is shown to achieve the lowest FDR for a given bias.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0
dc.titleOptimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips
dc.typeJournal Article
dc.identifier.doi10.1093/nar/gkq871
melbourne.affiliation.departmentMedical Biology (W.E.H.I.)
melbourne.affiliation.departmentSchool of Mathematics and Statistics
melbourne.affiliation.departmentSchool of Physics
melbourne.source.titleNucleic Acids Research
melbourne.source.volume38
melbourne.source.issue22
dc.rights.licenseCC BY-NC
melbourne.elementsid1208327
melbourne.contributor.authorSmyth, Gordon
melbourne.contributor.authorOshlack, Alicia
melbourne.contributor.authorShi, Wei
dc.identifier.eissn1362-4962
melbourne.accessrightsOpen Access


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