Figure 16.1 (Plate 2). A microarray image composed of red and green colour
channels. Here each spot represents a different probe molecule and the colour intensity
reflects the binding of DNA within two samples, each labelled with a different fluorescent
marker. Original image courtesy of Paul Edwards and Karen Howarth, University of
Cambridge.
Much of what we describe in this chapter relates to data management and many of the
underlying programming principles are the same as things that have been discussed
before. Hence the programming examples, which relate to array analyses, will focus on
the organisation and analysis of the data rather than its acquisition. We will assume that
the experiments have been done correctly and with due diligence, although some emphasis
will be put on the handling of errors or noise in the data. These Python examples will start
fairly simply, to illustrate the fundamental principles of what the data means and how we
represent it in computational data structures. Examples will grow more complex by the
incorporation of analytical methods, many of which are discussed in other chapters, e.g.
clustering data.
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