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+I simply need an example dataset similar to that you have. Just a quick look brings up GSE16200 as something that might be simple to play with. Normally, you would not need these lines and would start with the Analysis section.
+The 'eset' object is an ExpressionSet and contains the normalized gene expression measures as well as the sample
+Use the limma package for analysis. I am keeping it simple here, but adding multiple factors is just a little
+Now, make a heatmap of the top genes. Dumping out data for excel, making online reports, or pdfs like
+this one are straightforward. I often make large PDFs of all DE genes for collaborators to look at on
+their own. You can also export in a format that TreeView understands so that collaborators can explore
Binary file added.