Changes between Version 3 and Version 4 of SOPs/go_annotation

Timestamp:

12/12/16 11:43:33 (8 years ago)

Author:

gbell

Comment:

--

SOPs/go_annotation

@@ -20 +20 @@
      * If a gene list is not unique, duplicate genes can be given a //shared// weight, for eg. if a gene occurs four times in the list it is given a weight of 0.25, if it is unique a weight of 1 is given.
    2. Run GSEA: Tools -> GseaPreranked  
+   3. To run the same type of analysis on the command line, use a command like
+
+java -Xmx512m -cp /usr/lib/share/gsea2/gsea2-2.2.2.jar xtools.gsea.GseaPreranked -gmx gseaftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v5.2.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -rnk ./MY_COMPARISON.rnk -scoring_scheme weighted -rpt_label GSEA_out_v1 -chip gseaftp.broadinstitute.org://pub/gsea/annotations/GENE_SYMBOL.chip -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 2 -zip_report false -out GSEA_OUT.TEST_v1 -gui false
+
+
 
    ==== Unranked List ====