Fig 1 Unsupervised principal component analysis (PCA). A total of 204 experiments are selleckchem included in the three-dimensional PCA and each sphere represents the gene expression profile for a cell line or leukaemia sample. The signal used is DQN1. The first three … Fig 2 Analysis of intra- and inter-laboratory reproducibility. (A) Box-and-whisker plots display, for each laboratory, the intra-laboratory squared correlation coefficients (r2) of all probe sets represented on the HG-U133 Plus 2.0 microarray for the HepG2 … Inter-laboratory reproducibility of gene expression analyses As an example of inter-laboratory reproducibility of gene expression analyses, correlations between Centre 3 and all other ten laboratories are given (Fig 2C and D).

The degree of correlation was only slightly different to the intra-laboratory reproducibility (Fig 2C). The minimum and maximum mean values were 0?959 and 0?985, respectively. This again demonstrated a high inter-laboratory correlation of HepG2 gene expression profiles and confirms the outstanding performance of microarray analysis in the 11 centres. This high inter-laboratory consistency can be also shown in pairwise scatter plot analyses. The 5?0 ��g HepG2 replicate analysis between Centre 3 and other laboratories is shown as an example (Fig 2D). A very tight distribution of gene expression data can be observed along the diagonal line for every paired HepG2 sample. Additional analyses of inter-site correlations for HepG2 subsets across all laboratories, along with hierarchical cluster and principal component analyses, are given in Appendix SI.

Furthermore, the online section also contains an analysis of the relative contribution of different sources of both technical and biological variability in gene expression measurements. Discussion Taken together, this study demonstrated that standardizing experimental protocols for microarray analysis and performing a thorough operator training resulted in excellent comparability with respect to both data sets generated within a participating laboratory and across 11 different laboratories in three continents. This extends the observations of a recent across-platform comparison study from the Toxicogenomics Research Consortium (Bammler et al, 2005). In particular, and also noted by Bammler et al (2005), the standardization of RNA labelling protocols using common procedures was recognized as an important contributor to signal intensity correlations across different laboratories.

Our study further shows consistent results when compared with Anacetrapib the intra-platform precision demonstrated from three different centres in the recent MicroArray Quality Consortia data (Shi et al, 2006). In conclusion, this standardization effort represented the prerequisite foundation of the first phase of the MILE study, wherein 1889 patients have, thus far, been analysed by whole genome expression microarrays (Haferlach et al, 2006).