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Python for Bioinformatics by Kinser

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24 Gene Expression Array Files

Gene expression data (or microarrays) have quickly become an important component in modern bioinformatics. Microarray data is available on many websites in many formats. This chapter will consider the images generated by some microarray systems and develop Python codes to read them.

24.1 Raw Data

The gene expression array is a slide that contains several thousand spots of genes. A typical experiment will use two different sources, each with its own dye (commonly Cy3 and Cy5). The detection process creates an image for each dye that consists of circular spots of varying intensities. The intensity of a single spot indicates the amount of source that is attached to that particular spot on the slide. Since there are ...

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