Threshold Selection Study on Fisher Discriminant Analysis Used in Exon Prediction for Unbalanced Data Sets

Yutao Ma, Yanbing Fang, Ping Liu, Jianfu Teng

School of Electronic Information Engineering, Tianjin University, Tianjin, China.
School of Mathematics and Computer Science, Ningxia University, Yinchuan, China.
School of Physics and Electrical Information Engineering, Ningxia University, Yinchuan, China.

DOI: 10.4236/cn.2013.53B2108                

Abstract

In gene prediction, the Fisher discriminant analysis (FDA) is used to separate protein coding region (exon) from non-coding regions (intron). Usually, the positive data set and the negative data set are of the same size if the number of the data is big enough. But for some situations the data are not sufficient or not equal, the threshold used in FDA may have important influence on prediction results. This paper presents a study on the selection of the threshold. The eigen value of each exon/intron sequence is computed using the Z-curve method with 69 variables. The experiments results suggest that the size and the standard deviation of the data sets and the threshold are the three key elements to be taken into consideration to improve the prediction results.

Keywords

Fisher Discriminant Analysis; Threshold Selection; Gene Prediction; Z-Curve; Size of Data Set

Conflicts of Interest

The authors declare no conflicts of interest.

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