A statistical analysis of spot variation using the two-dimensional polyacrylamide gel electrophoresis |
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| Authors: | R Kuick E Boerwinkle S M Hanash C F Sing |
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| Affiliation: | 1. Department of Nematology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Lawley Road, Coimbatore 641 003, Tamil Nadu, India;2. Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India;3. Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India;4. Centre for Agricultural Nanotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India |
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| Abstract: | For the development of valid algorithms for matching protein spots between two-dimensional gels, it is essential that one has an understanding of the relative roles of the many sources of variability affecting the location of spots. We first consider the contribution of observers to the measurement variability of spot location, arriving at a simple model for these effects. Next we present an analysis of the variability in spot locations for a sample of gels containing duplicate gels for each sample. Our data indicate that both differences between duplicates and between samples are considerable, and that the size of the effects depends on the region of the gel being considered. In the discussion we examine several matching strategies that match large groups of gels based on algorithms which match two gels at a time. |
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