Background correction of two-colour cDNA microarray data using spatial smoothing methods |
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Authors: | André Schützenmeister Hans-Peter Piepho |
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Institution: | (1) Bioinformatics Unit, Institute for Crop Production and Grassland Research, University of Hohenheim, Fruwirthstrasse 23, 70599 Stuttgart, Germany |
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Abstract: | The analysis of two-colour cDNA microarray data usually involves subtracting background values from foreground values prior
to normalization and further analysis. This approach has the advantage of reducing bias and the disadvantage of blowing up
the variance of lower abundant spots. Whenever background subtraction is considered, it implicitly assumes locally constant
background values. In practice, this assumption is often not met, which casts doubts on the usefulness of simple background
subtraction. In order to improve background correction, we propose local background smoothing within the pre-processing pipeline
of cDNA microarray data prior to background correction. For this purpose, we employ a geostatistical framework with ordinary
kriging using both isotropic and anisotropic models of spatial correlation and 2-D locally weighted regression. We show that
application of local background smoothing prior to background correction is beneficial in comparison to using raw background
estimates. This is done using data of a self-versus-self experiment in Arabidopsis where subsets of differentially expressed
genes were simulated. Using locally smoothed background values in conjunction with existing background correction methods
increases the power, increases the accuracy and decreases the number of false positive results. |
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Keywords: | |
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