Nimgaonkar Ashish, Sanoudou Despina, Butte Atul J, Haslett Judith N, Kunkel Louis M, Beggs Alan H, Kohane Isaac S
Informatics Program, Children's Hospital, Harvard Medical School, Boston, MA, USA.
BMC Bioinformatics. 2003 Jun 25;4:27. doi: 10.1186/1471-2105-4-27.
The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays are regularly modified to incorporate new genes and improved target sequences. Although the ability to compare datasets across generations is crucial for any long-term research project, to date no means to allow such comparisons have been developed. In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips (HuGeneFL and HG-U95A) was measured.
Correlation coefficients were computed for gene expression values across chip generations based on different measures of similarity. Comparing the absolute calls assigned to the individual probe sets across the generations found them to be largely unchanged.
We show that experimental replicates are highly reproducible, but that reproducibility across generations depends on the degree of similarity of the probe sets and the expression level of the corresponding transcript.
大规模基因表达谱分析技术的发展正在迅速改变生物学研究的规范。但这种快速的变化本身也带来了挑战。商业微阵列会定期进行修改，以纳入新基因和改进的靶序列。尽管对于任何长期研究项目而言，跨代比较数据集的能力至关重要，但迄今为止尚未开发出进行此类比较的方法。在本研究中，我们测定了两代Affymetrix基因芯片（HuGeneFL和HG-U95A）上基因表达水平的可重复性。
基于不同的相似性度量，计算了跨芯片代的基因表达值的相关系数。比较两代中分配给各个探针集的绝对调用，发现它们基本未变。
我们表明实验复制品具有高度可重复性，但跨代的可重复性取决于探针集的相似程度以及相应转录本的表达水平。
