de Reyniès Aurélien, Geromin Daniela, Cayuela Jean-Michel, Petel Fabien, Dessen Philippe, Sigaux François, Rickman David S
Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France.
BMC Genomics. 2006 Mar 15;7:51. doi: 10.1186/1471-2164-7-51.
We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip, GE Healthcare CodeLink and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program.
All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms.
We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels.
我们比较了从三种不同的最先进的商业短寡核苷酸和长寡核苷酸微阵列平台（Affymetrix基因芯片、通用电气医疗集团CodeLink和安捷伦科技公司）获得的表达测量的相对精度和准确性。比较的设计旨在在多项目计划的背景下对每个平台进行评估。
所有湿实验室实验和原始数据采集均由每个商业平台独立进行。使用来自所有可用靶标的测量值评估平台内的可重复性。相对信号强度的平台间比较基于一组约3400个共同且无冗余的靶标，这些靶标因其与单个转录本的独特对应关系而被选中。尽管有许多强烈相似性的例子，但我们发现不同平台之间存在几个差异领域。
我们发现与安捷伦的双色阵列相比，基于单色的微阵列（Affymetrix和CodeLink）具有更高的可重复性水平。总体而言，Affymetrix数据与样本匹配的实时定量逆转录聚合酶链反应（QRT-PCR）数据的一致性水平略高，特别是在检测基因表达水平的微小变化方面。
