Python Programming for Biology: Bioinformatics and Beyond

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.