Microarray studies

Jolly, R. A. et al., Pooling Samples Within Microarray Studies A Comparative Analysis of Rat Liver Transcription Response to Prototypical Toxicants, Physiol. Genomics, 22, 346, 2005. 

The typical cDNA microarray study can be described in nine steps (1) establishing an appropriate experimental design (2) isolation and conversion of mRNA to labeled cDNA (3) hybridization of labeled cDNA to the microarray slide (4) image acquisition, (5) data storage, (6) normalization (7) statistical analysis (8) data mining and (9) validation of the results. Each of these steps is multifaceted and the introduction of error at any point in the process can lead to costly loss of data. The following section describes the steps followed in experimental design. 

Liang M, Briggs AG, Rute E, Greene AS, Cowley AW. 2003. Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies. Physiol Genomics 14 199. 

Substrates for the creation of protein microarrays were initially selected from those used for DNA arrays, for example, PLL glass slides. At first, these substrates proved to be sufficient for antibody microarray studies. However, not all proteins will behave well or similarly on a particular substrate material. New solid phases applicable for protein microarrays need to be found. 

AB, Switzerland) in SPR (surface plasmon resonance) studies. The PLL-PEG-biotin-sAV was used for microarray studies as described for the commercial product. A detailed description of the design and physical and chemical characterization of the PLL-grafted PEG monolayer is provided by Ruiz-Taylor et al. (2001). 

Kerr MK (2003) Design considerations for efficient and effective microarray studies. Biometrics 59 822-828... 

Shao Y, Tseng CH (2007) Sample size calculation with dependence adjustment for FDR-control in microarray studies. Stat Med 26 4219-4237. doi 10.1002/sim.2862... 

Qiu W, Lee MLT, Whitmore GA (2008) Sample size and power calculation in microarray studies using the sizepower package. Technical report, Bioconductor... 

Pavlidis P (2003) Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31 282-289. doi S1046202303001579 (pii)... 

Table 10 Normalization Methods Commonly Used in Microarray Studies...

Large-Scale Microarray Studies of Gene Expression in Multiple Regions of the Brain in Schizophrenia and Alzeimer s Disease... 

Some early studies demonstrated the potential of the new technology [39-41] to examine the differences between normal and malignant colonic tissue [39] and identifying potential subclassifications of breast cancer [41]. An interesting aside to these studies was the different analytical methods used by the authors to analyze and interpret the data. This variability of approach remains a feature of microarray studies and can hinder the comparison of data from different studies. However, there are now processes in place which attempt to standardize at least some of the analyses [42],... 

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