#File:"params-EG3.1-test-2+FC-ALL.map" #"Standard MRR processing" #"Revised: 5-02-2009" #"GBS: Mon Sep 28 15:13:49 EDT 2009" # -addPrologue:"ParamScripts/prologMRR.html" -addEpilogue:"ParamScripts/epilogueMRR.html" -addRowNumbers # -addTableName:"mAdb Microarray Retrieval Report - All Samples" # -mapDollarsigns:$$TITLE$$,"mAdb Microarray Retrieval Report - All Samples" -mapDollarsigns:$$TEST_OR_ALL$$,"All samples for" -mapDollarsigns:$$TISSUE$$,"Muscle" -mapDollarsigns:$$TESTNAME$$,"EG3.1-test-2+FC-ALL" -mapDollarsigns:$$PAGE_LABEL$$,"Stat5MKO+GH vs Stat5MKO-GH" -mapDollarsigns:$$DESCRIPTION$$,"Muscle cells from Stat5-null 12-week mice with GH treatment and 15 week Stat5-null without GT treatment" -mapDollarsigns:$$GBS_DESCRIPTION$$,"Muscle: EG003.1+EG003.2
(T3+)  Stat5MKO+GH vs Stat5MKO-GH --- fold changes > 2X and p-Value<0.05" -mapDollarsigns:$$TESTNAME$$,"EG3.1-test-2+FC-ALL" -mapDollarsigns:$$CLASS_A$$,"Samples[Stat5MKO+GH]: EG003.1-01, EG003.1-02, EG003.1-05" -mapDollarsigns:$$CLASS_B$$,"Samples[Stat5MKO-GH]: EG003.2-04, EG003.2-05, EG003.2-06" # -hdrMapName:"A Mean","A Mean (Stat5MKO+GH)" -hdrMapName:"B Mean","B Mean (Stat5MKO-GH)" # -inputDir:InputTree/CellTissue/Muscle -outputDir:Analyses/Muscle -tableDir:data.Table/ -files:"EG3.1-test-2+FC-ALL.txt" # -joinTableFile:"EG3.1-test-2+FC.txt" # #"Limit the number of rows to the highest 500 fold-change values" -limitMaxTableRows:"500,A-B Mean Difference,Descending" # -allowHdrDups -alternateRowBackgroundColor:white -rmvTrailingBlankRowsAndColumns #-shrinkBigCells:25,-5 -shrinkBigCells:1,-5 -hdrLines:2 -hasEmptyLineBeforeTable -makePrefaceHTML -mapOptionsLists # #"Map header names. Select from field='Affy .CEL file (16)'" #" to field= 'GSP ID (9)' or 'Simple GSP ID (10)'" -mapHdrNames:"data.Table//EGMAP.map,Affy .CEL file (16),GSP ID (9)" # #"Drop some of the columns" -dropColumnColumn:"mgB36 Chr:Start-Stop" -dropColumn:"mgB36 Cytoband" -dropColumn:Annotation_Src -dropColumn:UniGene -dropColumn:RefSeq -dropColumn:Refseqs_Hit -dropColumn:geneIDS_Hit -dropColumn:"Entrez GeneID" -dropColumn:"Locus Tag" -dropColumn:"BioCarta Pathways" -dropColumn:"KEGG Pathways" # (Add # if want to keep) #-dropColumn:"Gene Ontology Terms" -dropColumn:"GO Tier2 Component" -dropColumn:"GO Tier3 Component" -dropColumn:"GO Tier2 Function" -dropColumn:"GO Tier3 Function" -dropColumn:"GO Tier2 Process" -dropColumn:"GO Tier3 Process" #"The following was added 5/28/09" -dropColumn:"Map" -dropColumn:"mgB37_Probe Chr:Start-Stop" -dropColumn:"mgB37_Probe Cytoband" -dropColumn:"mgB37_RefSeq Chr:Start-Stop" -dropColumn:"mgB37_RefSeq Cytoband" # #"Reorder columns to left side of Table" -reorderColumn:Gene,1 -reorderColumn:"A-B Mean Difference",2 -reorderColumn:Difference,3 -reorderColumn:"A Mean",4 -reorderColumn:"B Mean",5 -reorderColumn:"A-B p-Value",6 -reorderColumn:"p-Value",7 -reorderColumn:"Well ID",8 -reorderColumn:"Feature ID",9 -reorderColumn:"Description",10 # #"Sort rows by column - use whichever comes first" -sortRowsByColumn:"A-B Mean Difference",Descending -sortRowsByColumn:Difference,Descending -sortRowsByColumn:p-Value,Ascending -sortRowsByColumn:Gene,Ascending # #"These map mAdb Feature Report data to Bioinformatics databases" -hrefData:"Well ID",http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A -hrefData:Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene= -hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset= # #"----------- end --------- "