Performance evaluation of ranking methods for relevant gene selection in cancer microarray datasets

Authors:
Manju Sardana;Baljeet Kaur;R. K. Agrawal
Affiliations:
School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India;Hansraj College, Delhi University, Delhi, India;School of Computer and Systems Sciences, Jawaharlal Nehru University, New Delhi, India
Venue:
MICAI'12 Proceedings of the 11th Mexican international conference on Advances in Artificial Intelligence - Volume Part I
Year:
2012

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Abstract

Microarray data is often characterized by high dimension and small sample size. Gene ranking is one of the most widely explored techniques to reduce the dimension because of its simplicity and computational efficiency. Many ranking methods have been suggested which depict their efficiency dependent upon the problem at hand. We have investigated the performance of six ranking methods on eleven cancer microarray datasets. The performance is evaluated in terms of classification accuracy and number of genes. Experimental results on all dataset show that there is significant variation in classification accuracy which depends on the choice of ranking method and classifier. Empirical results show that Brown Forsythe test statistics and Mutual Information method exhibit high accuracy with few genes whereas Gini Index and Pearson Coefficient perform poorly in most cases.