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Why is it important to have similar (even) hybridization signal intensities from Cy3 and Cy5?

April 26, 2017cy3 cy5 hybridization intensities signal similar

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Why is it important to have similar (even) hybridization signal intensities from Cy3 and Cy5?

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Differential gene expression analysis with microarrays relies on comparison between two different mRNA populations on the same slide. It is important to prepare both probes in as similar fashion as possible to eliminate experimental artefacts. Hence even incorporation of CyDye is important. Furthermore, not all microarray scanners can detect both Cy3 and Cy5 equally well.