Wilson Claire L, Pepper Stuart D, Hey Yvonne, Miller Crispin J
Paterson Institute for Cancer Research, Withington, Manchester, UK.
Biotechniques. 2004 Mar;36(3):498-506. doi: 10.2144/04363RN05.
The desire to perform microarray experiments with small starting amounts of RNA has led to the development of a variety of protocols for preparing and amplifying mRNA. This has consequences not only for the standardization of experimental design, but also for reproducibility and comparability between experiments. Here we investigate the differences between the Affymetrix standard and small sample protocols and address the data analysis issues that arise when comparing samples and experiments that have been processed in different ways. We show that data generated on the same platform using different protocols are not directly comparable. Further, protocols introduce systematic biases that can be largely accounted for by using the correct data analysis techniques.
使用少量起始RNA进行微阵列实验的需求促使了多种制备和扩增mRNA方案的发展。这不仅对实验设计的标准化有影响，而且对实验之间的可重复性和可比性也有影响。在这里，我们研究了Affymetrix标准方案和小样本方案之间的差异，并解决了在比较以不同方式处理的样本和实验时出现的数据分析问题。我们表明，在同一平台上使用不同方案生成的数据不能直接进行比较。此外，方案会引入系统性偏差，而使用正确的数据分析技术在很大程度上可以对此加以解释。
