Microarray analysis begins once images have been scanned and .tif files have been obtained for the arrays. Scanning produces two .tif image files. One represents the Cy5 readings and one the Cy3 readings. Both of these files are loaded together into ImaGene for quantification of each spot.
The current version of ImaGene is 9.0. This software allows each spot on the microarray to be quantified. What this means is, each spot will have an intensity value assigned to it. Briefly, the Cy5 and Cy3 files are loaded into the software and are overlaid onto one another. A template is then constructed (or a saved one is used). Various optimization steps are carried out allowing the quantification procedure to be as accurate as possible. At this point it is worth mentioning that loading of a template (or creating one) also allows the gene identifiers to be loaded. This makes it possible to know exactly which spot on the array is corresponding to which gene.
Once optimization is complete, quantification is automatically carried out via the software. The results are saved as .txt files. The files can now be loaded into a data analysis software e.g. GeneSpring.
To view a basic protocol for ImaGene, click here.
To view frequently asked questions on ImaGene, click here.