Gupta Rashi, Ruosaari Salla, Kulathinal Sangita, Hollmén Jaakko, Auvinen Petri
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
Mol Cell Probes. 2007 Oct-Dec;21(5-6):321-8. doi: 10.1016/j.mcp.2007.03.006. Epub 2007 Apr 6.
The DNA microarray technique allows monitoring the expression levels of thousands of genes simultaneously. A single DNA microarray experiment involves a number of error-prone manual and automated processes, which influence the results and have an impact on the subsequent stages of analysis. Typical problems of arrays are pinning errors while probe printing and the corruption of spots by noise patches. These errors should be detected at the time of image analysis in order to prevent the erroneous intensities from ending up in the analysis and inference stages.
In this paper we introduce the concept (referred to as SybrSpot) of utilizing information provided by an additional dye, SYBR green RNA II, for segmentation of gene expression microarrays. Owing to the effective binding of the SYBR green RNA II to the array probes, an image with high signal-to-noise ratio is obtained. This image is used to learn about the spot quality and to flag spots which are not reliably hybridized and corrupted by noise. Further, we compare SybrSpot with GenePix and demonstrate that SybrSpot performs better than GenePix when flagging spots with no probes or weak probes.
The code is available upon request to authors.
DNA微阵列技术能够同时监测数千个基因的表达水平。单次DNA微阵列实验涉及许多容易出错的手动和自动化流程，这些流程会影响结果，并对后续分析阶段产生影响。阵列的典型问题包括探针打印时的点样错误以及噪声斑块对斑点的破坏。这些错误应在图像分析时被检测出来，以防止错误的强度进入分析和推理阶段。
在本文中，我们引入了利用额外的染料SYBR green RNA II提供的信息来分割基因表达微阵列的概念（称为SybrSpot）。由于SYBR green RNA II与阵列探针的有效结合，获得了具有高信噪比的图像。该图像用于了解斑点质量，并标记未可靠杂交且被噪声破坏的斑点。此外，我们将SybrSpot与GenePix进行了比较，结果表明在标记无探针或弱探针的斑点时，SybrSpot比GenePix表现更好。
可根据作者要求提供代码。
