#File:params-MRR-noMap.map #"Revised: 4-4-2009" # -addPrologue:data.MRR/prolog.html -addEpilogue:data.MRR/epilogue.html -addRowNumbers -addTableName:"mAdb Microarray Retrieval Report" -inputDir:data.MRR -outputDir:html/data.MRR -tablesDir:data.Table # -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" #"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" # #-dropColumn:"Gene Ontology Terms" (remove # if want to drop) -dropColumn:"GO Tier2 Component" -dropColumn:"GO Tier3 Component" -dropColumn:"GO Tier2 Function" -dropColumn:"GO Tier3 Function" -dropColumn:"GO Tier2 Process" -dropColumn:"GO Tier3 Process" # #"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:"Entrez GeneID",http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids= -hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset= # #"----------- end --------- "