Cancer Res Treat.  2007 Jun;39(2):74-81.

An Attempt for Combining Microarray Data Sets by Adjusting Gene Expressions

• Kim KY
• Kim SH
• Ki DH
• Jeong J
• Jeong HJ
• Jeung HC
• Chung HC
• Rha SY

Abstract

PURPOSE: The diverse experimental environments in microarray technology, such as the different platforms or different RNA sources, can cause biases in the analysis of multiple microarrays. These systematic effects present a substantial obstacle for the analysis of microarray data, and the resulting information may be inconsistent and unreliable. Therefore, we introduced a simple integration method for combining microaray data sets that are derived from different experimental conditions, and we expected that more reliable information can be detected from the combined data set rather than from the separated data sets.
MATERIALS AND METHODS
This method is based on the distributions of the gene expression ratios among the different microarray data sets and it transforms, gene by gene, the gene expression ratios into the form of the reference data set. The efficiency of the proposed integration method was evaluated using two microarray data sets, which were derived from different RNA sour-ces, and a newly defined measure, the mixture score.
RESULTS
The proposed integration method intermixed the two data sets that were obtained from different RNA sources, which in turn reduced the experimental bias between the two data sets, and the mixture score increased by 24.2%. A data set combined by the proposed method preserved the inter-group relationship of the separated data sets.
CONCLUSION
The proposed method worked well in adjusting systematic biases, including the source effect. The ability to use an effectively integrated microarray data set yields more reliable results due to the larger sample size and this also decreases the chance of false negatives.

Keyword

Microarray; Gene expression; Integration method; Different platforms; Different RNA sources; Systematic effects

MeSH Terms

Bias (Epidemiology)
Dataset*
Gene Expression*
RNA
Sample Size
RNA

Figure

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  Fig. 1 Boxplots for the expression ratios of a randomly selected gene. Boxplots for the expression ratios of a randomly selected gene in both the normal and tumor groups from two different data sets and a transformed data set (normal_A, tumor_A, normal_B and tumor_B: the normal and tumor groups in data set A and data set B, respectively; normal_A' and tumor_A': the normal and tumor groups in transformed data set A).

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  Fig. 2 Density plots of 20 randomly selected genes. Density plots of 20 randomly selected genes from the data set comprising the normal group (red: data set A, black: data set B, blue: transformed data set). The horizontal and vertical axes represent the gene expression values and relative frequency, respectively.

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  Fig. 3 Density plots and scatter plot matrix of the two principal components. Density plots and scatter plot matrix of the two principal components (A) in data set A and data set B and (B) in the transformed data set and data set B (blue: data set A, red: data set B).

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  Fig. 4 Dendrogram for the two data sets. Dendrogram for the two data sets prior to (A) and after (B) the integration method. The Euclidean distance was used as a similarity measure and the average linkage method was used in this work.

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