Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities

Abstract

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is a low-sensitivity measure to obtain high expression values which would be saturated in a high-sensitivity measure; the second, by the converse strategy, obtains additional information about the low-expression levels. Two mathematical models based on linear and gamma curves are presented for relating the two measurements to each other and producing a coherent and extended range of values. The procedure minimizes the quantization relative error and avoids the collateral effects of saturation. Since most of the current scanner devices are able to adjust the saturation level, the strategy can be considered as a universal solution, and not dependent on the image processing software used for reading the DNA chip. Various tests have been performed, on both proprietary and public domain data sets, showing a reduction of the saturation and quantization effects, not achievable by other methods, with a more complete description of gene-expression data and with a reasonable computational complexity.

Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies

“…Notably, the highest Pearson correlation was obtained for the two sequencing-based technologies (0.951; P Ͻ 0.01), which might be due to the saturated hybridization signals in the array data sets (see Fig. S3 in the supplemental material) (14).…”

“…Moreover, many of the probes associated with 36 of these 40 genes revealed saturated hybridization signals in the array data sets (see Fig. S3 in the supplemental material), suggesting that they were inaccurately measured by the array due to falling outside the dynamic range of the array technology (14). This observation implies that RNA sequencing exceeds the depth of analysis of the traditional array technologies, especially for genes that are expressed at a high level.…”

Repeated Measurements on Distinct Scales With Censoring—A Bayesian Approach Applied to Microarray Analysis of Maize

“…It has been only recently that some attention has been focused on analytical methods that might permit incorporating multiple slide scans obtained under different measurement conditions into statistical analyses. Several approaches have been proposed in the literature for doing so (Dudley et al 2002; Lyng et al 2004; Garcia de la Nava et al 2004). None of these approaches, however, can incorporate an arbitrary and possibly different number of scans per slide into the analysis.…”

“…This means that there was no improvement of the dynamic range of expression estimates by Romualdi et al (2003). Dudley, Aach, Steffen, and Church (2002) and Garcia de la Nava, van Hijum, and Trelles (2004) used multiple slide readings at varying settings to extend the dynamic range and address the censoring error. However, the former used only the estimate from one reading for each gene (possibly linearly transformed) whereas the latter accommodated only two scans.…”

Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome

“…Microarrays contain a number of error-sources (Ramdas, Coombes, Baggerly et al 2001), some of them physical (quenching (Kubista, 1994; Randolph and Waggoner, 1997)), some chemical (hybridization), some related to the electronics (gating (Schäferling and Nagl, 2006), dynamic range (de la Nava, van Hijum and Trelles, 2006), saturation (Lyng, Badiee, Svendsrud et al 2004)). In most microarray experiments the measurement errors remain unknown, but they are widely believed to follow Lorentz distributions (Press, Teukolsky, Vetterling et al 2003; Brody, Williams, Wod et al 2002).…”