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genepix [2010/05/30 19:35]
genepix [2017/05/24 10:36] (current)
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 +====== GenePix ======
 +[[GenePix]] is a //multiplatform// microarray scanning system. It is developed by [[http://www.moleculardevices.com|Molecular Devices]] and includes their own **scanner** machines together whit their own **image analysis software**.
 +This system produces [[GPR]] files which are the one of the [[raw data]] file types that [[Babelomics]] normalization tools can handle.
 +  *http://www.moleculardevices.com
 +  *[[http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr|GPR files]]: produced by their image analysis software. These files are the [[raw data]] files in [[Babelomics]] normalization tools.
 +  *[[http://www.moleculardevices.com/pages/instruments/microarray_main.html|GenePix Microarray Scanner Systems]]
 +  *[[http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html|All GenePix File Formats]]
 +  *[[http://www.moleculardevices.com/pages/software/gn_genepix_pro.html|GenePix Microarray Image Analysis Software]]
 +====== Two Color Platforms ======
 +When analyzing [[spotted arrays]] microarray scanning software produces a picture of the glass. An **image analysis** program is needed afterwards to transform //pixel// information from the picture into an spot intensity measurement which will reflect gene expression. Through this process each spot in the array has to be recognized in the picture, that is, some //pixels// in the image have to be assigned to the spot. The light intensity of those //pixels// is summarized into a unique measurement (usually the mean) and referred to as the **[[foreground]]** measurement of the spot. There are some other //pixels// "around" the spot which are also summarized into a single value (usually the median) know as the **[[background]]** intensity of the spot. This  **[[background]]** values are used to correct for non specific binding.
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