Open Access Highly Accessed Methodology article

Optimized LOWESS normalization parameter selection for DNA microarray data

John A Berger1*, Sampsa Hautaniemi2, Anna-Kaarina Järvinen3, Henrik Edgren34, Sanjit K Mitra1 and Jaakko Astola2

Author Affiliations

1 Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106-9560, USA

2 Institute of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland

3 Biomedicum Biochip Center, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland

4 Medical Biotechnology Group, VTT Technical Research Center of Finland and University of Turku, P.O. Box 106, 20521 Turku, Finland

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BMC Bioinformatics 2004, 5:194  doi:10.1186/1471-2105-5-194

Published: 9 December 2004

Abstract

Background

Microarray data normalization is an important step for obtaining data that are reliable and usable for subsequent analysis. One of the most commonly utilized normalization techniques is the locally weighted scatterplot smoothing (LOWESS) algorithm. However, a much overlooked concern with the LOWESS normalization strategy deals with choosing the appropriate parameters. Parameters are usually chosen arbitrarily, which may reduce the efficiency of the normalization and result in non-optimally normalized data. Thus, there is a need to explore LOWESS parameter selection in greater detail.

Results and discussion

In this work, we discuss how to choose parameters for the LOWESS method. Moreover, we present an optimization approach for obtaining the fraction of data points utilized in the local regression and analyze results for local print-tip normalization. The optimization procedure determines the bandwidth parameter for the local regression by minimizing a cost function that represents the mean-squared difference between the LOWESS estimates and the normalization reference level. We demonstrate the utility of the systematic parameter selection using two publicly available data sets. The first data set consists of three self versus self hybridizations, which allow for a quantitative study of the optimization method. The second data set contains a collection of DNA microarray data from a breast cancer study utilizing four breast cancer cell lines. Our results show that different parameter choices for the bandwidth window yield dramatically different calibration results in both studies.

Conclusions

Results derived from the self versus self experiment indicate that the proposed optimization approach is a plausible solution for estimating the LOWESS parameters, while results from the breast cancer experiment show that the optimization procedure is readily applicable to real-life microarray data normalization. In summary, the systematic approach to obtain critical parameters in the LOWESS technique is likely to produce data that optimally meets assumptions made in the data preprocessing step and thereby makes studies utilizing the LOWESS method unambiguous and easier to repeat.