A model-based analysis of microarray experimental error and normalisation

Y. Fang
<span title="2003-08-15">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
A statistical model is proposed for the analysis of errors in microarray experiments and is employed in the analysis and development of a combined normalisation regime. Through analysis of the model and two-dye microarray data sets, this study found the following. The systematic error introduced by microarray experiments mainly involves spot intensity-dependent, feature-speci®c and spot position-dependent contributions. It is dif®cult to remove all these errors effectively without a suitable
more &raquo; ... bined normalisation operation. Adaptive normalisation using a suitable regression technique is more effective in removing spot intensity-related dye bias than self-normalisation, while regional normalisation (block normalisation) is an effective way to correct spot position-dependent errors. However, dye-¯ip replicates are necessary to remove feature-speci®c errors, and also allow the analyst to identify the experimentally introduced dye bias contained in non-self-self data sets. In this case, the bias present in the data sets may include both experimentally introduced dye bias and the biological difference between two samples. Self-normalisation is capable of removing dye bias without identifying the nature of that bias. The performance of adaptive normalisation, on the other hand, depends on its ability to correctly identify the dye bias. If adaptive normalisation is combined with an effective dye bias identi®cation method then there is no systematic difference between the outcomes of the two methods.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gng097">doi:10.1093/nar/gng097</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12907748">pmid:12907748</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC169988/">pmcid:PMC169988</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uql62kfdezafpipbbuwemv2cwi">fatcat:uql62kfdezafpipbbuwemv2cwi</a> </span>
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