Abstract
Background:
Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array.
Results:
Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure.
Conclusions:
The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.
Publication types
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Comparative Study
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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Arabidopsis / genetics
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DNA, Complementary / genetics
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DNA, Plant / genetics
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DNA, Protozoan / genetics
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Databases, Genetic / statistics & numerical data
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Gene Expression Profiling / methods*
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Gene Expression Profiling / standards*
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Gene Expression Profiling / statistics & numerical data
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Gene Expression Regulation
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Gene Expression Regulation, Plant
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Normal Distribution
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Oligonucleotide Array Sequence Analysis / methods*
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Oligonucleotide Array Sequence Analysis / standards*
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Oligonucleotide Array Sequence Analysis / statistics & numerical data
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Plasmodium falciparum / genetics
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Research Design / standards
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Research Design / statistics & numerical data
Substances
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DNA, Complementary
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DNA, Plant
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DNA, Protozoan