"Harshlighting" small blemishes on microarrays -: art. no. 65
"Harshlighting" small blemishes on microarrays -: art. no. 65
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DOI：
10.1186/1471-2105-6-65
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发表时间：
2005-03-22
影响因子：
3
通讯作者：
Wittkowski, KM
中科院分区：
文献类型：
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作者：
Suárez-Fariñas, M;Haider, A;Wittkowski, KM
背景资料：显微镜工作者熟悉荧光图像可能由于灰尘和碎片、玻璃瑕疵、流体或表面涂层的不均匀分布等而产生的许多瑕疵。微阵列扫描显示出类似的伪影，这些伪影会影响分析，特别是当人们试图检测细微变化时。然而，大多数瑕疵是很难找到的肉眼，特别是在高密度寡核苷酸阵列（HDONAs）。结果：我们提出了一种方法，利用统计功率提供了几个HDONAs，这是在类似的条件下，除了实验因素。这种方法“harshlights”瑕疵，使他们明显。我们发现经验，我们的芯片约有25%的污点，我们分析屏蔽它们筛选差异表达的基因的影响。结论：实验试图评估微妙的表达变化，应仔细筛选芯片上的污点。所提出的方法为研究人员提供了一种新的强大的方法来提高微阵列分析的灵敏度。通过在基于模型的分析之前利用拓扑信息来识别和掩蔽瑕疵，该方法防止伪影混淆背景校正、归一化和概括的过程。
Background: Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs).Results: We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes.Conclusion: Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.