Overview of the Mouse Example :: Microarray Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Overview of the Mouse Example

The microarray data used in this example is available in a web supplement to the paper by Brown et al. from

http://labs.pharmacology.ucla.edu/smithlab/index.html

The microarray data is also available on the Gene Expression Omnibus Web site at

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30

The GenePix GPR formatted file mouse_a1pd.gpr contains the data for one of the microarrays used in the study. This is data from voxel A1 of the brain of a mouse in which a pharmacological model of Parkinson's disease (PD) was induced using methamphetamine. The voxel sample was labeled with Cy3 (green) and the control, RNA from a total (not voxelated) normal mouse brain, was labeled with Cy5 (red). GPR formatted files provide a large amount of information about the array, including the mean, median, and standard deviation of the foreground and background intensities of each spot at the 635 nm wavelength (the red, Cy5 channel) and the 532 nm wavelength (the green, Cy3 channel).

Example: Visualizing Microarray Data

Exploring the Microarray Data Set