Abstract
Microarray data is inherently noisy due to the noise contaminated from various sources during the preparation of microarray slide and thus it greatly affects the accuracy of the gene expression. How to eliminate the effect of the noise constitutes a challenging problem in microarray analysis. Efficient denoising is often a necessary and the first step to be taken before the image data is analyzed to compensate for data corruption and for effective utilization for these data. Hence preprocessing of microarray image is an essential to eliminate the background noise in order to enhance the image quality and effective quantification. Existing denoising techniques based on transformed domain have been utilized for microarray noise reduction with their own limitations. The objective of this paper is to introduce novel preprocessing techniques such as optimized spatial resolution (OSR) and spatial domain filtering (SDF) for reduction of noise from microarray data and reduction of error during quantification process for estimating the microarray spots accurately to determine expression level of genes. Besides combined optimized spatial resolution and spatial filtering is proposed and found improved denoising of microarray data with effective quantification of spots. The proposed method has been validated in microarray images of gene expression profiles of Myeloid Leukemia using Stanford Microarray Database with various quality measures such as signal to noise ratio, peak signal to noise ratio, image fidelity, structural content, absolute average difference and correlation quality. It was observed by quantitative analysis that the proposed technique is more efficient for denoising the microarray image which enables to make it suitable for effective quantification.
Highlights
It is well known that microarray technology can monitor thousand of DNA sequences in a high density array on a glass [1]
The proposed method has been validated in microarray images of gene expression profiles of Myeloid Leukemia using Stanford Microarray Database with various quality measures such as signal to noise ratio, peak signal to noise ratio, image fidelity, structural content, absolute average difference and correlation quality
In this paper we present two novel preprocessing techniques, namely optimized spatial resolution and spatial domain filtering to eliminate the noise in microarray that helps in more accurate estimation of the intensity of spots to determine the expression level
Summary
It is well known that microarray technology can monitor thousand of DNA sequences in a high density array on a glass [1]. Each microscopic spot represents a single gene This technology enables to measure the level of activity of thousands of genes simultaneously and monitor the whole genome on a single chip so that researchers can have a big picture of the interactions among those genes simultaneously. In the basic procedure for a microarray experiment two mRNA samples are reversetranscribed into cDNA, labeled using different fluorescent dyes (e.g., the red fluorescent dye Cy5 and the green fluorescent dye Cy3), mixed and hybridized with the arrayed DNA sequences. After this competitive hybridization, the slides are imaged using a scanner which makes fluorescence measurement for each dye.
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