Impact of pixel intensity correlations on statistical inferences of expression levels in cDNA microarray experiments

Binu, VS and Nair, Sreekumaran N and Prasad, Manjunath K and Kalesh, KM (2015) Impact of pixel intensity correlations on statistical inferences of expression levels in cDNA microarray experiments. International Journal of Bioinformatics Research and Applications, 11 (3). pp. 257-267.

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Abstract

In a cDNA microarray experiment, the final measurement is intensity ratio at a spot in the microarray chip. The objective of the present study is to estimate the uncertainty associated with the final intensity ratio at each spot in cDNA microarray chips and also to explore the role of pixel intensity correlations in statistical inferences of gene expression levels. We estimate uncertainty at each spot using the theory of error propagation under two different situations: (1) when there is no correlation between pixel intensities and (2) when the pixel intensities are positively correlated. The inverses of these estimated uncertainties are used as weights in downstream analysis to test the significance of each gene. The analysis was verified on a data downloaded from the GEO database. Our study shows that the uncertainty and statistical inference of gene expression levels depend on correlation between pixel intensities within a spot.

Item Type: Article
Uncontrolled Keywords: Uncertainty; estimation; pixel intensity correlation; microarray; statistical inference; gene expression level.
Subjects: Departments at MU > Statistics
Depositing User: KMC Manipal
Date Deposited: 30 Apr 2015 06:58
Last Modified: 30 Apr 2015 06:58
URI: http://eprints.manipal.edu/id/eprint/142568

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