Changes between Version 5 and Version 6 of SOPs/go_annotation


Ignore:
Timestamp:
02/28/17 16:32:27 (8 years ago)
Author:
thiruvil
Comment:

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  • SOPs/go_annotation

    v5 v6  
    2121   2. Run GSEA: Tools -> GseaPreranked 
    2222   3. To run the same type of analysis on the command line, use a command like
    23 
     23{{{
    2424java -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
    25 
     25}}}
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