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Open Access Methodology article

Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data

Cecilia Ritz and Patrik Edén*

Author Affiliations

Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, Sweden

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BMC Genomics 2008, 9:25  doi:10.1186/1471-2164-9-25

Published: 19 January 2008

Abstract

Background

For 2-dye microarray platforms, some missing values may arise from an un-measurably low RNA expression in one channel only. Information of such "one-channel depletion" is so far not included in algorithms for imputation of missing values.

Results

Calculating the mean deviation between imputed values and duplicate controls in five datasets, we show that KNN-based imputation gives a systematic bias of the imputed expression values of one-channel depleted spots. Evaluating the correction of this bias by cross-validation showed that the mean square deviation between imputed values and duplicates were reduced up to 51%, depending on dataset.

Conclusion

By including more information in the imputation step, we more accurately estimate missing expression values.