Parameter	Value	DataType	Comments
unigeneURL	http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?ORG=Hs&TEXT=	String	UNIGENE by Clone_ID server
IMAGE2unigeneURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Hs&CLONE=	String	lookup UNIGENE from CloneID
IMAGE2GeneBankURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Hs&ACC=	String	lookup GeneBank from CloneID [FUTURE]
IMAGE2GIDURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Hs&GID=	String	lookup GeneBank GID from CloneID [FUTURE]
MAX_GRIDS	4	int	# grids
MAX_GRID_COLS	24	int	# columns
MAX_GRID_ROWS	23	int	# rows
gipoFile	GIPO-mAdb-printset-8.txt	File	from mAdb
samplesDBfile	Samples-db.txt	File	from mAdb
MAX_FIELDS	1	int	# replicate spots/clone
FIELD_LAYOUT	LtoR	String	fields are Left to Right [Future]
GRID_LAYOUT	Horizontal	String	Grids are Left To Right  [Future]
GRID_PER_ROW	1	int	# Grids per Row in each field [Future]
FIELDS_ARE_NUMBERED	TRUE	boolean	Contains field number else just cycles in file [Future]
MAX_INTENSITY	65535	int	max raw intensity - scale larger values to this value
G1	0	int	"min intensity range, scroller"
G2	65535	int	"max intensity range, scroller"
SpotRadius	5	int	"(2 to 20 pixels) 50 microns, scroller"
clusterDistThr	10	float	"0.0 to 40.0, scroller"
nbrOfClustersThr	6	int	default # clusters for NPN-clustering
pValueThr	0.2	float	default p-value for statistical tests
spotCVthr	0.25	float	default spot CV value
CanvasHorSize	1100	int	"pixels, size of microarray image "
CanvasVertSize	1100	int	"pixels, size of microarray image "
dataBase	mAdb Hs-OC-2-23Cx24R DB	String	name of the database
maAnalysisProgram	mAdb DB	String	quantitation program
proxyServer	http://www-lecb.ncifcrf.gov/cgi-bin/maeProxySvr?	String	LECB server to get outside stuff
writeFileCGIurl	http://www-lecb.ncifcrf.gov/cgi-bin/maeSaveFile?	String	LECB state saving server
geneBankCloneURL	http://www.ncbi.nlm.nih.gov/irx/cgi-bin/submit_form_query?TITLE=dbEST+Retrieval+Output&INPUTS=1&BRACKETS=NONE&ADDFLAGS=-b&DB=dbest&NDOCS=10&Q1=	String	GeneBank by Clone_ID NCBI server
geneBankCloneURLepilogue	[clin]	String	Q1=1247496%5Bclin%5D' encodes 'Q1=1247496[clin]
dbEstURL	http://www.ncbi.nlm.nih.gov/irx/cgi-bin/birx_doc?dbest+	String	dbEst NCBI server
geneBankAccURL	http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&Dopt=g&uid=	String	GeneBankAcc NCBI
mAdbURL	http://nciarray.nci.nih.gov/cgi-bin/clone_report.cgi?CRITERIA=clone&PARAMETER=	String	"mAdb clone page, J.Powell [Future]"
jaxURL	http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:	String	Jackson Lab Clone_ID map base address
GeneCardURL	http://bioinfo.weizmann.ac.il/cards-bin/carddisp?	String	GeneCard DB
histologyURL	**NONE**	String	histology DB
modelsURL	**NONE**	String	models DB
userName		String	generic
canSaveFileFlag	FALSE	boolean	[FUTURE] no state saving for now
noMsgReporting	TRUE	boolean	No incremental LOADING reports
reuseXYcoords	TRUE	boolean	Reuse XY coords from first probe
usePseudoXYcoords	TRUE	boolean	use pseudo XY coord image - no XY data
useRatioData	TRUE	boolean	"Treat F1, F2 as ratio (F1/F2)"
useRatioData	TRUE	boolean	"Treat F1, F2 as ratio (F1/F2)"
swapRowsColumns	FALSE	boolean	Flip array rows and columns
maxPreloadImages	4	int	max # HPS to start with unless overide
maxClonesReported	50	int	max # of clones to report
makeAllCmdsActiveFlag	FALSE	boolean	grayed out
geneClassNamesFile	GeneClassNames-mAdb.txt	File	from lemkin
geneIdNameClassFile	GeneIdNameClass-mAdb.txt	File	[FUTURE] from  mAdb
maInfoFile	MaExplorerInfo-mAdb-Hs-OC-2px-4Bx24Cx23R.txt	File	from HP .txt files
geneClassListNamesFile	GeneClassListOfNames-mAdb.txt	File	[FUTURE] from mAdb
calibDNAname		String	Calibration DNA - if any
yourPlateName		String	name of researcher's clones - if any
classNameX	HP-X 'set'	String	name of HP-X probe set
classNameY	HP-Y 'set'	String	name of HP-Y probe set
mapTF	"GipoTable,grid,GipoTable,Block"	String	map MAE to user field
mapTF	"GipoTable,grid row,GipoTable,Row"	String	map MAE to user field
mapTF	"GipoTable,grid col,GipoTable,Column"	String	map MAE to user field
mapTF	"GipoTable,Clone ID,GipoTable,ID"	String	map MAE to user field
mapTF	"GipoTable,GeneName,GipoTable,Name"	String	map MAE to user field
mapTF	"QuantTable,RawIntensity1,QuantTable,Cy3RI"	String	map MAE to user field
mapTF	"QuantTable,RawIntensity2,QuantTable,Cy5RI"	String	map MAE to user field
mapTF	"QuantTable,Background1,QuantTable,BkgrdCy3"	String	map MAE to user field
mapTF	"QuantTable,Background2,QuantTable,BkgrdCy5"	String	map MAE to user field
mapTF	"QuantTable,grid,QuantTable,grid"	String	map MAE to user field
mapTF	"QuantTable,grid row,QuantTable,grid row"	String	map MAE to user field
mapTF	"QuantTable,grid col,QuantTable,grid col"	String	map MAE to user field
flourescentLbl1	Cy3	String	name of dye for flouresent label 1
flourescentLbl2	Cy5	String	name of dye for flouresent label 2
SubMenu1	mAdb experimental human data	String	HP sub menu
SubMenu2	Other 1	String	HP sub menu
SubMenu3	Other 2	String	HP sub menu
SubMenu4	Other 3	String	HP sub menu
HelpMenu1	NCI/DCS mAdb home page	String	Help sub menu URL
HelpMenu2	CIT/BIMAS home page	String	Help sub menu URL
HelpMenu3	MAExplorer home page	String	Help sub menu URL
HelpURL1	http://nciarray.nci.nih.gov/	String	Help sub menu URL
HelpURL2	http://bimas.cit.nih.gov/	String	Help sub menu URL
HelpURL3	http://www.lecb.ncifcrf.gov/MAExplorer/	String	Help sub menu URL
EditDate	"07-19-00, Lemkin"	String	using JP mAdb experimental server mouse data