Changes between Version 32 and Version 33 of SOPs/go_annotation

Timestamp:

04/22/21 11:18:57 (4 years ago)

Author:

gbell

Comment:

--

SOPs/go_annotation

@@ -49 +49 @@
         * 3. Click on  "Tools -> GseaPreranked"  
         * 4. Select one of the gene sets from the "Gene sets database". We recommend starting with the Hallmarks set (h.all). You can find more information about the sets [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|here ]]
-        * 5. Select your uploaded ranked list and click the run button.
+        * 5. Select your uploaded ranked list (rnk file) for "Ranked list".
+        * 6. The "Chip platform" refers to the type of identifiers in your rnk file.  If your input file has human gene symbols, choose a platform file like "Human_Gene_Symbol_with_Remapping_MSigDB*.chip".  If your input input file has mouse gene symbols, you'll need to choose a "platform" to assign the mouse symbols to human symbols (like Mouse_Gene_Symbol_Remapping_to_Human_Orthologs_MSigDB*.chip)
+        * 7. Click the "Show" button next to "Basic fields" to name your sample/comparison.  This is especially important, of course, if you're running GSEA multiple times.  You can also set the output directory. 
+        * 8. Click "Run" at the bottom of the GSEA window.  It usually takes at least several minutes.  If you see "Error!" near the bottom left, click on it to diagnose what went wrong.
 
      *  To run the same type of analysis on the command line, you can see the command the GUI used clicking the "Command" button and run that command in your Linux machine.