Changes between Version 2 and Version 3 of net.sf.basedb.reggie/notes427


Ignore:
Timestamp:
May 18, 2020, 8:55:39 AM (7 months ago)
Author:
Nicklas Nordborg
Comment:

Added instructions for adding SSP models to reggie-config.xml

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  • net.sf.basedb.reggie/notes427

    v2 v3  
    2525== B. Update Reggie ==
    2626
    27 Update Reggie to version 4.27 as usual. Do not forget to run the Installation wizard.
     27Update Reggie to version 4.27. Add the following models to the `<rscript>/<ssp>/<models>` section
     28in `reggie-config.xml` (remove the `<model>` entry that is already there). Do not forget to run the Installation wizard.
    2829
    29 
     30{{{
     31<model name="Subtype" annotation-type="SSP_Subtype" annotation-type-scores="SSP_Subtype_Scores">
     32        Training_Run19081Genes_noNorm_SSP.PAM50subtype4Most.Fcc15_5x5foldCV.num.rules.50_21.selRules.AIMS.GS.RData
     33</model>
     34<model name="PAM50 subtype" annotation-type="SSP_PAM50subtype" annotation-type-scores="SSP_PAM50subtype_Scores">
     35        Training_Run19081Genes_noNorm_SSP.subtypeMost.Fcc15_5x5foldCV.num.rules.50_24.selRules.AIMS.GS.Rdata
     36</model>
     37<model name="ROR asT0" annotation-type="SSP_RORasT0" annotation-type-scores="SSP_RORasT0_Scores">
     38        Training_Run19081Genes_noNorm_SSP.scaled.ROR.tot.asT0.c005.Fcc15_5x5foldCV.num.rules.50_21.selRules.AIMS.GS.RData
     39</model>
     40<model name="ER" annotation-type="SSP_ER" annotation-type-scores="SSP_ER_Scores">
     41        Training_Run19081Genes_noNorm_SSP.ER_v2.Fcc15_5x5foldCV.num.rules.50_19.selRules.AIMS.GS.RData
     42</model>
     43<model name="PR" annotation-type="SSP_PR" annotation-type-scores="SSP_PR_Scores">
     44        Training_Run19081Genes_noNorm_SSP.PR_v2.Fcc15_5x5foldCV.num.rules.50_3.selRules.AIMS.GS.Rdata
     45</model>
     46<model name="ERBB2" annotation-type="SSP_ERBB2" annotation-type-scores="SSP_ERBB2_Scores">
     47        Training_Run19081Genes_noNorm_SSP.HER2.Fcc15_5x5foldCV.num.rules.50_8.selRules.AIMS.GS.RData
     48</model>
     49<model name="CC15" annotation-type="SSP_CC15" annotation-type-scores="SSP_CC15_Scores">
     50        Training_Run19081Genes_noNorm_SSP.CClusterK20_15_5x5foldCV.num.rules.50_27.selRules.AIMS.GS.Rdata
     51</model>
     52<model name="IntClust10" annotation-type="SSP_IntClust10" annotation-type-scores="SSP_IntClust10_Scores">
     53        Training_Run19081Genes_noNorm_SSP.iC10.mimic_5x5foldCV.num.rules.50_41.selRules.AIMS.GS.RData
     54</model>
     55}}}
    3056