MOTIVATION: Microarray experiments with thousands of genes on a slide and multiple slides used in any experimental set represent a large body of data with many sources of variation. The identification of such sources of variation within microarray experimental sets is critical for correct deciphering of desired gene expression differences. RESULTS: We describe new methods for the normalization using spatial mixed models which include splines and analysis of two-colour spotted microarrays for within slide variation and for a series of slides. The model typically explains 45-85% of the variation on a slide with only approximately 1% of the total degrees of freedom. The results from our methods compare favourably with those from intensity dependent normalization loess methods where we accounted for twice as much uncontrolled and unwanted variation on the slides. We have also developed an index for each EST that combines the various measures of the differential response into a single value that researchers can use to rapidly assess the genes of interest.
MOTIVATION: Microarray experiments with thousands of genes on a slide and multiple slides used in any experimental set represent a large body of data with many sources of variation. The identification of such sources of variation within microarray experimental sets is critical for correct deciphering of desired gene expression differences. RESULTS: We describe new methods for the normalization using spatial mixed models which include splines and analysis of two-colour spotted microarrays for within slide variation and for a series of slides. The model typically explains 45-85% of the variation on a slide with only approximately 1% of the total degrees of freedom. The results from our methods compare favourably with those from intensity dependent normalization loess methods where we accounted for twice as much uncontrolled and unwanted variation on the slides. We have also developed an index for each EST that combines the various measures of the differential response into a single value that researchers can use to rapidly assess the genes of interest.
Authors: Pamela A Knight; Susan E Griffith; Alan D Pemberton; Judith M Pate; Lauren Guarneri; Katherine Anderson; Richard T Talbot; Sarah Smith; David Waddington; Mark Fell; Alan L Archibald; Stewart T G Burgess; David W Smith; Hugh R P Miller; Ivan W Morrison Journal: Vet Res Date: 2011-06-17 Impact factor: 3.683
Authors: Raphaël Kiekens; Annelies Vercauteren; Beatrijs Moerkerke; Els Goetghebeur; Hilde Van Den Daele; Roel Sterken; Martin Kuiper; Fred van Eeuwijk; Marnik Vuylsteke Journal: Nucleic Acids Res Date: 2006-08-02 Impact factor: 16.971
Authors: Orla M Keane; Amonida Zadissa; Theresa Wilson; Dianne L Hyndman; Gordon J Greer; David B Baird; Alan F McCulloch; Allan M Crawford; John C McEwan Journal: BMC Genomics Date: 2006-03-06 Impact factor: 3.969