Microarray Quality Control project

Controls Consortium (Baker ef al., 2005)], and MAQC [Microarray Quality Control Project (http //www.fda.gov/nctr/science/centers/toxicoinfor-matics/maqc/)]. However, these guidelines tend to focus on documentation of some analytical details or use control nucleotides that do not broadly represent the full dynamic range of the array and fall short of really addressing the technical issues in these types of analyses (Draghici et al., 2006 Shields, 2006). 

MAQC Consortium (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9) 1151-1161... 

Patterson TA et al (2006) Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 24 1140-1150. doi nbtl242 (pii)10.1038/nbtl242... 

Quality Assurance/Quality Control parameter and metrics to ensure data reproducibility, e.g. the establishment of calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms (see also MAQC project http //w w w.nature. com/nbt/focus/maqc/). 

Several projects and consortia were established in order to solve the above-mentioned problems, e.g., the Micro Array Quality Control (MAQC) project, led by US FDA, which main goal is to assess microarray study variability and to develop standards and quality measures for transcriptomics data [50, 51], Another research project, the human embryonic stem cell-derived novel alternative test systems (ESNATS) recently published a paper to address similar questions using human embryonic stem cell-based in vitro test systems for reproductive toxicity by transcriptomics analysis [52], The strong aspect of this study, that it transparently presents difficulties, such as batch effects, and provides analysis strategies including overrepresented transcription factors. It can be used as basis for further development of reproductive toxicity assays based on transcriptomics analysis. 

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