Analysis of microarray data - VSN International

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54Analysis of Microarray Data in GenStatTwo-way clusteringThis menu combines the previous two menus to allowyou to jointly cluster on both probes/genes andtargets/slides. A map of the two-way array ofexpression can then be displayed as a shade plot, whichshows the pattern of differential expression. Using theexample data saved in “Data13-6-9.gwb”, open theStats | Microarray | Cluster | Two-way menu to get thedialog to the right. Use the corrected log-ratios from thecolumn cLogRatio, and enter the Probe and Slideinformation from the columns Name and Sliderespectively. Completing the dialog as shown. Using ahierarchical clustering, only the top 1% of probes withthe groups thresholds set to 98% for Probes and 100% for Targets (i.e.do not group any slides together), and setting the options as shown tothe right, we obtain the dendrograms shown below (one for probes(below left) and another for slides (below right)) and the shade plotshowing the group means by slides (bottom right).
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.
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Analysis of microarray data - VSN International

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