How to do an integrated analysis of microarray data?
Here is brief tutorial. Open a file (either an EXCEL file or a tab-delimited, or comma-delimited file) that contains your microarray data. It might be a good idea to start with the sample data file (yeast200.xls) included in the AMADA distribution. The 200 means that it includes only the first 200 loci. It should be found in the installation directory of AMADA. This is a subset of yeast data that I found at Stanford web site. Click Analysis|Clustering. A dialog box will appear for you to specify options. The yeast200.xls file contains no missing values, so you should uncheck the Has missing value checkbox (it is on by default). Choose one of the seven implemented distance/similarity measures and one of the three clustering algorithms and click the OK button. AMADA will now run to carry out a cluster analysis and expose additional functions after the cluster analysis is finished. A progress bar indicates the progress of the execution. After a few seconds or a few minutes, depending on t
