Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data.
Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data.
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DOI：
10.1186/1471-2164-6-72
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发表时间：
2005-05-11
期刊：
影响因子：
4.4
通讯作者：
Werner-Washburne M
中科院分区：
文献类型：
--
作者：
Timlin JA;Haaland DM;Sinclair MB;Aragon AD;Martinez MJ;Werner-Washburne M
商业微阵列扫描仪和软件不能区分光谱重叠的发射源，因此不能准确地鉴定或校正不是源自标记的cDNA的发射。我们采用了我们的高光谱微阵列扫描仪加上多变量数据分析算法，独立地识别和定量的排放从所有来源的调查三个文物，降低微阵列数据的准确性和可靠性：偏向绿色通道，染料分离，和可变的背景排放。在这里，我们证明了几种常见的微阵列文物的存在下，而不是标记的cDNA，可以显着改变阵列数据的准确性和可靠性的排放源。本研究中使用的微阵列代表了目前基因组研究中使用的广泛的微阵列。这些发现加强了对细节的仔细关注的需要，以识别并随后消除或量化微阵列图像中外来发射的存在。高光谱扫描与多变量分析一起提供了对杂交后微阵列发射源的独特而详细的理解。这种同时识别和定量微阵列中的污染物和背景排放的机会显著提高了数据的可靠性和准确性，并允许以前无法实现的微阵列排放的质量控制水平。使用这些工具，我们不仅可以量化外来排放源对信号的影响程度和贡献，还可以确定未能解释它们的后果，并获得必要的洞察力来调整制备方案，以防止此类问题的发生。
Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cDNA. We employed our hyperspectral microarray scanner coupled with multivariate data analysis algorithms that independently identify and quantitate emissions from all sources to investigate three artifacts that reduce the accuracy and reliability of microarray data: skew toward the green channel, dye separation, and variable background emissions. Here we demonstrate that several common microarray artifacts resulted from the presence of emission sources other than the labeled cDNA that can dramatically alter the accuracy and reliability of the array data. The microarrays utilized in this study were representative of a wide cross-section of the microarrays currently employed in genomic research. These findings reinforce the need for careful attention to detail to recognize and subsequently eliminate or quantify the presence of extraneous emissions in microarray images. Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.
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影响因子：
2.1
作者：
Murphy, D
通讯作者：
Murphy, D
DOI：
10.1109/memb.2002.1032647
发表时间：
2002-07-01
影响因子：
--
作者：
Huebschman, ML;Schultz, RA;Garner, HR
通讯作者：
Garner, HR
影响因子：
2.4
作者：
Van Benthem, MH;Keenan, MR;Haaland, DM
通讯作者：
Haaland, DM
DOI：
10.1073/pnas.161242998
发表时间：
2001-07-31
影响因子：
11.1
作者：
Brown, CS;Goodwin, PC;Sorger, PK
通讯作者：
Sorger, PK
影响因子：
2.7
作者：
Hegde, P;Qi, R;Quackenbush, J
通讯作者：
Quackenbush, J