DNA array analysis in a Microsoft® Windows® environment
DNA array analysis in a Microsoft® Windows® environment
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DOI：
10.2144/02321bc02
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发表时间：
2002-01-01
期刊：
影响因子：
2.7
通讯作者：
McKibben, L
中科院分区：
文献类型：
--
作者：
Conway, T;Kraus, B;McKibben, L
基于Microsoft（R）Windows（R）的计算机已经发展到这样的程度，它们为DNA阵列数据的鲁棒分析提供了足够的计算和可视化能力。事实上，较小的实验室可能更喜欢在Windows环境中进行部分或全部分析和可视化，而不是在UNIX等替代平台上。我们开发了一系列用Visual Basic for Microsoft Excel（R）电子表格编写的手动执行的宏，允许快速和全面的基因表达数据分析。第一个宏将基因名称分配给DNA阵列上的点，并通过将每个基因的信号强度表示为所有基因强度的百分比来归一化单个杂交。第二个宏简化了对实验重复组的个体基因测量的置信度的统计考虑，通过用学生t检验计算概率值。第三个宏引入阈值，计算实验条件之间的表达比率，并计算对数比率值的平均值的标准偏差。选定的数据列由第四个宏复制，以创建适合于输入到Microsoft Access数据库中的经处理的数据集。描述了Access数据库结构，其允许跨多个实验的简单查询和将数据导出到第三方数据可视化软件包中。这些分析工具可以在他们目前的形式使用的其他工作与商业E。大肠杆菌膜阵列，或者它们可以适于与其它系统一起使用。带有嵌入式Visual Basic宏的Excel电子表格及其使用的详细说明可从http://www.ou.edu/microarray获得。
Microsoft(R) Windows(R)-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel(R) spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the stint of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access(R) database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available tit http://www.ou.edu/microarray.