Parameter	Value	DataType	Comments
MAX_FIELDS	2	int	# replicate spots ResGen
MAX_GRIDS	8	int	# grids ResGen
MAX_GRID_COLS	24	int	# cols/grid ResGen
MAX_GRID_ROWS	9	int	# rows/grid ResGen
MAX_INTENSITY	65535	int	max raw intensity - scale larger values to this value
I1	0	int	"min intensity range, scroller"
I2	65535	int	"max intensity range, scroller"
SpotRadius	6	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	MGAP DB	String	name of the database
maAnalysisProgram	Pathways 2.01	String	quantitation program
proxyServer	http://www-lecb.ncifcrf.gov/cgi-bin/maeProxySvr?	String	LECB server to get outside stuff (only for LECB)
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
unigeneURL	http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?ORG=Mm&TEXT=	String	UNIGENE by Clone_ID server
mAdbURL	http://nciarray.nci.nih.gov/cgi-bin/clone_report.cgi?CRITERIA=clone&PARAMETER=IMAGE:	String	mAdb clone page
GeneCardURL	http://bioinfo.weizmann.ac.il/cards-bin/carddisp?	String	GeneCard DB
histologyURL	http://mammary.nih.gov/models/	String	MGAP histology DB
modelsURL	http://mammary.nih.gov/models/	String	MGAP models DB
IMAGE2unigeneURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Mm&CLONE=IMAGE:	String	lookup UNIGENE from CloneID
IMAGE2GeneBankURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Mm&ACC=IMAGE:	String	lookup GeneBank from CloneID [FUTURE]
IMAGE2GIDURL	http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?ORG=Mm&GID=IMAGE:	String	lookup GeneBank GID from CloneID [FUTURE]
userName		String	generic
maxPreloadImages	0	int	max # HPs to start with
maxClonesReported	50	int	max # of clones to report
makeAllCmdsActiveFlag	FALSE	boolean	grayed out
flourescentLbl1	Cy3	String	name of dye for flouresent label 1 (not used)
flourescentLbl2	Cy5	String	name of dye for flouresent label 2 (not used)
swapRowsColumns	TRUE	boolean	Flip array rows and columns
useRatioData	FALSE	boolean	"Treat F1, F2 as ratio (F1/F2)"
ignoreExtraFields	FALSE	boolean	"ignore extra explicit 'field"" entries"
gipoFile	GIPO-MGAP.txt	File	Composite MGAP GIPO file
samplesDBfile	public-SamplesDB-MGAP.txt	File	MGAP public sample database
maAnalysisProgram	Research Genetics Pathways 2.01	String	quantification program used
calibDNAname	m. g. DNA	String	name of Calibration DNA
yourPlateName	your plate	String	name of researcher's clones
classNameX	HP-X 'set'	String	name of HP-X probe set
classNameY	HP-Y 'set'	String	name of hP-Y probe set
HelpMenu1	List of hybrdization probes	String	Help sub menu URL
HelpMenu2	MGAP animal models	String	Help sub menu URL
HelpMenu3	MGAP home page	String	Help sub menu URL
HelpURL1	http://www.lecb.ncifcrf.gov/mae/maeHybridizations.html	String	Help sub menu URL
HelpURL2	http://mammary.nih.gov/models/	String	Help sub menu URL
HelpURL3	http://mammary.nih.gov/	String	Help sub menu URL
mapTF	"GipoTable,plate,GipoTable,plate"	String	map MAE to user field
mapTF	"GipoTable,plate row,GipoTable,plate row"	String	map MAE to user field
mapTF	"GipoTable,plate col,GipoTable,plate col"	String	map MAE to user field
mapTF	"GipoTable,grid,GipoTable,grid"	String	map MAE to user field
mapTF	"GipoTable,grid row,GipoTable,grid row"	String	map MAE to user field
mapTF	"GipoTable,grid col,GipoTable,grid col"	String	map MAE to user field
mapTF	"GipoTable,Clone ID,GipoTable,Clone ID"	String	map MAE to user field
mapTF	"GipoTable,GeneName,GipoTable,GeneName"	String	map MAE to user field
EditDate	"01-13-01, Lemkin"	String	simplified for use as example