#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 --------- "