Evaluating the performance of microarray segmentation algorithms
Evaluating the performance of microarray segmentation algorithms
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DOI：
10.1093/bioinformatics/btl502
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发表时间：
2006-12-01
期刊：
影响因子：
5.8
通讯作者：
Yli-Harja, Olli
中科院分区：
文献类型：
--
作者：
Lehmussola, Antti;Ruusuvuori, Pekka;Yli-Harja, Olli
动机：虽然已经开发了许多算法用于微阵列分割，但算法之间的广泛比较却很少受到关注。在这项研究中，我们评估了九个微阵列分割算法的性能。使用模拟和真实的微阵列实验，我们克服了性能评估的挑战，所产生的缺乏地面实况信息。使用模拟实验，使我们能够分析的分割精度在一个单一的像素水平上，通常在传统的图像处理研究。通过真实的实验，我们间接地测量了分割性能，确定了算法之间的显着差异，并研究了所得到的基因表达data.Results的特点：总体而言，我们的结果表明算法之间存在明显的差异。结果表明分割性能如何取决于图像质量，哪些算法在显著不同的性能水平上操作，以及分割算法的选择如何影响差异表达基因的识别。
Motivation: Although numerous algorithms have been developed for microarray segmentation, extensive comparisons between the algorithms have acquired far less attention. In this study, we evaluate the performance of nine microarray segmentation algorithms. Using both simulated and real microarray experiments, we overcome the challenges in performance evaluation, arising from the lack of ground-truth information. The usage of simulated experiments allows us to analyze the segmentation accuracy on a single pixel level as is commonly done in traditional image processing studies. With real experiments, we indirectly measure the segmentation performance, identify significant differences between the algorithms, and study the characteristics of the resulting gene expression data.Results: Overall, our results show clear differences between the algorithms. The results demonstrate how the segmentation performance depends on the image quality, which algorithms operate on significantly different performance levels, and how the selection of a segmentation algorithm affects the identification of differentially expressed genes.