Systematic evaluation of scaling methods for gene expression data

Gaurav Pandey, Lakshmi Naarayanan Ramakrishnan, Michael S Steinbach, Vipin Kumar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Even after an experimentally prepared gene expression data set has been pre-processed to account for variations in the microarray technology, there may be inconsistencies between the scales of measurements in different conditions. This may happen for reasons such as the accumulation of gene expression data prepared by different laboratories into a single data set. A variety of scaling and transformation methods have been used for addressing these scale inconsistencies in different studies on the analysis of gene expression data sets. However, a quantitative estimation of their relative performance has been lacking. In this paper, we report an extensive evaluation of scaling and transformation methods for their effectiveness with respect to the important problem of protein function prediction. We consider several such commonly used methods for gene expression data, such as z-score scaling, quantile normalization, diff transformation, and two new scaling methods, sigmoid and double sigmoid, that have not been used previously in this domain to the best of our knowledge. We show that the performance of these methods can vary significantly across data sets, but Dsigmoid scaling and z-score transformation generally perform well for the two types of gene expression data, namely temporal and non-temporal, respectively.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages376-381
Number of pages6
DOIs
StatePublished - 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

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    Pandey, G., Ramakrishnan, L. N., Steinbach, M. S., & Kumar, V. (2008). Systematic evaluation of scaling methods for gene expression data. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 376-381). [4684923] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.33