Analysis of microarray data - VSN International

Analysis of Microarray Data in GenStat 55Two-channel microarray exampleThe following example shows how to analysedata from a two-channel microarray experiment.The data in this experiment are from a mouseknock out experiment with 6384 genes perslide. There were 16 slides, 8 control mice and 8knockout mice all on the red dye compared to astandard reference on the green dye. Note thatthis design is not dye balanced, as there are nodye swaps, as the reference is always on red.The data are stored in the file ApoAISlides.csvthat can be found in the Microarrays folder (asexplained on page 2). The file can be opened inGenStat by selecting Open from the File menuand then navigating to and selecting the filename.When a CSV file is opened in GenStat, youhave the option of opening it into a textwindow, or into a spreadsheet. In this example,the data are to be opened into a spreadsheet: thiscan be done by clicking on the Read button asshown right.On opening CSV files, you are prompted with two dialogswhere additional options can be specified to control howthe data are opened. The first dialog (as shown right) hasoptions for controlling which rows of the data are to beopened. For this example, the whole file is read byclicking on the OK button.The second dialog contains further options for controllinghow the data are to be opened including data typeconversion and location of column names. For theexample, the default settings can be used by clicking onthe OK button.