[BioC] Format identification

Daniel Brewer daniel.brewer at icr.ac.uk
Wed Jan 3 13:02:30 CET 2007 

Hello,

Could anyone help me identify the format of this microarray data file?
Here are the first few lines:

TYPE	text	text	text	text	text	integer	integer	float	float	float
float	float	text	float	float	float	float	float	float	text	text
integer	float	float	float	float	float	float	float	float	text	text
integer	float	float	float	float	float	float	float	integer	float
integer	text	text	integer	float	float	integer	text	text	integer
integer	float	float	integer	float	text	text	integer	float	float
float	float	integer	text	text	text	text	text	text	text	text
FEPARAMS	FeatureExtractor_UserName	FeatureExtractor_ComputerName
FeatureExtractor_ExtractionTime	SpotFinder	SpotFinder_Version
SpotFinder_NumRows	SpotFinder_NumCols	SpotFinder_DevLimit
SpotFinder_ROIW	SpotFinder_ROIH	SpotFinder_NomSpotWidth
SpotFinder_NomSpotHeight	CornerMethod	CornerUL_x	CornerUL_y
CornerUR_x	CornerUR_y	CornerLL_x	CornerLL_y	CalcSpotStats
CalcSpotStats_Version	CalcSpotStats_RejectMethod
CalcSpotStats_StatBoundFeat	CalcSpotStats_StatBoundBG
CalcSpotStats_CookieWidth	CalcSpotStats_CookieHeight
CalcSpotStats_BGInnerWidth	CalcSpotStats_BGInnerHeight
CalcSpotStats_BGOuterWidth	CalcSpotStats_BGOuterHeight	OutlierFlagger
OutlierFlagger_Version	OutlierFlagger_NonUnifOLOn
OutlierFlagger_FeatATerm	OutlierFlagger_FeatBTerm
OutlierFlagger_FeatCTerm	OutlierFlagger_BGATerm
OutlierFlagger_BGBTerm	OutlierFlagger_BGCTerm
OutlierFlagger_ConfIntPValue	OutlierFlagger_PopnOLOn
OutlierFlagger_IQRatio	OutlierFlagger_MinPopulation	BGSubtractor
BGSubtractor_Version	BGSubtractor_BGSubMethod	BGSubtractor_MaxPVal
BGSubtractor_WellAboveMulti	BGSubtractor_BackgroundCorrectionOn
DyeNorm	DyeNorm_Version	DyeNorm_SelectMethod	DyeNorm_CorrMethod
DyeNorm_RankTolerance	DyeNorm_LOWESSSmoothFactor
DyeNorm_LOWESSNumSteps	DyeNorm_LOWESSDelta	Ratio	Ratio_Version
Ratio_ErrorModel	Ratio_AddErrorRed	Ratio_AddErrorGreen
Ratio_MultErrorRed	Ratio_MultErrorGreen	Ratio_UseSurrogates
FeatureExtractor	FeatureExtractor_Version	FeatureExtractor_ArrayName
FeatureExtractor_ScanFileName	FeatureExtractor_ScanFileGUID
FeatureExtractor_Barcode	FeatureExtractor_DesignFileName
FeatureExtractor_PrintingFileName
DATA	Administrator	AGILENT_SCANNER	Friday, May 21, 2004 13:36:01
14f32760-122b-11d3-a2d2-080009b996f0	Version A.6.1.1   Sep 11 2002
16:45:52	119	156	6.	17.27415	18.	9.	9.	Manual Lock Corners
35.7460789453694	28.5232645165563	2280.7885295609	45.2267119316202
23.210547849786	1798.37437653287	0b39b733-1912-11d3-a2d4-080009b996f0
Version A.6.1.1   Sep 11 2002 16:46:08	3	1.42	1.42	5.85	5.85	10.8
10.8	90.	90.	abfc1cb9-f631-11d4-83d0-0010b5093402	Version A.6.1.1   Sep
11 2002 16:48:13	1	5.e-002	320.	600.	9.e-002	320.	600.	1.e-003	1
1.42	15	82594834-4ac3-11d3-a4b8-00108302b7fe	Version A.6.1.1   Sep 11
2002 16:47:00	5	1.e-002	2.6	1	eef493ec-9143-11d3-a4e6-00108302b7fe
Version A.6.1.1   Sep 11 2002 16:47:20	6	1	5.e-002	0.25	2	0.
de2375cb-7605-11d3-a4e1-00108302b7fe	Version A.6.1.1   Sep 11 2002
16:47:49	0	30.	30.	9.e-002	9.e-002	1
4da119ff-f377-11d2-a2c8-080009b996f0	Version A.6.1.1   Sep 11 2002
16:49:03	RedPMT30 _16000526007828_S01_A02	D:\Penny\RedPMT30
_16000526007828_S01_A02	efe74bc5-ab11-11d8-a817-000103e1c41f
16000526007828_A02	E:\\000526_d_20030121.xml	E:\\000526_P_866_20030918.xml
*
TYPE	float	float	float	integer	float	float	float	integer	integer
float	float	integer	float	float	integer	integer	float	float	integer
float	float	integer	integer	integer	integer	integer	float	float
float	float	integer	integer	integer	integer	float	float	float	float
float	float	float	float	float	float	float	integer	float	integer
float	float	float	float	float
STATS	gDarkOffsetAverage	gDarkOffsetMedian	gDarkOffsetStdDev
gDarkOffsetNumPts	rDarkOffsetAverage	rDarkOffsetMedian
rDarkOffsetStdDev	rDarkOffsetNumPts	gNumSatFeat	gLocalBGInlierAve
gLocalBGInlierSDev	gLocalBGInlierNum	gGlobalBGInlierAve
gGlobalBGInlierSDev	gGlobalBGInlierNum	rNumSatFeat	rLocalBGInlierAve
rLocalBGInlierSDev	rLocalBGInlierNum	rGlobalBGInlierAve
rGlobalBGInlierSDev	rGlobalBGInlierNum	gNumFeatureNonUnifOL
gNumPopnOL	gNumNonUnifBGOL	gNumPopnBGOL	gOffsetUsed
gGlobalFeatInlierAve	gGlobalFeatInlierSDev	gGlobalFeatInlierNum
rNumFeatureNonUnifOL	rNumPopnOL	rNumNonUnifBGOL	rNumPopnBGOL
rOffsetUsed	rGlobalFeatInlierAve	rGlobalFeatInlierSDev
rGlobalFeatInlierNum	AllColorPrcntSat	AnyColorPrcntSat
AnyColorPrcntFeatNonUnifOL	AnyColorPrcntBGNonUnifOL
AnyColorPrcntFeatPopnOL	AnyColorPrcntBGPopnOL	TotalPrcntFeatOL
gNumNegBGSubFeat	gBGAdjust	rNumNegBGSubFeat	rBGAdjust
gLinearDyeNormFactor	rLinearDyeNormFactor	DyeNormDimensionlessRMS
DyeNormUnitWeightedRMS
DATA	23.677	24	4.70738	1000	23.97	24	6.44354	1000	0	276.944	18.3738
10855	276.944	18.3738	10855	0	197.602	17.5954	12570	197.602	17.5954
12570	90	9	125	2322	117.818	613.491	291.313	13087	144	12	197	605
76.0909	694.52	445.697	13030	0	0	1.0999	1.50193	0.0986118	19.5858
1.09116	87	15.9298	40	-9.31923	3.92258	2.37225	0.206798	0.0402023
*
TYPE	integer	integer	integer	text	text	text	integer	integer	text
text	text	text	float	float	float	float	float	float	float	boolean
boolean	float	float	float	float	integer	integer	integer	integer
integer	integer	float	float	float	float	float	float	integer	integer
float	float	float	float	float	float	integer	integer	boolean	boolean
float	float	boolean	boolean	boolean	boolean	boolean	boolean	boolean
boolean	boolean	float	float	float	float	float	boolean	boolean	float
float	integer	integer	boolean	boolean	float	float	float	float	float
boolean	float	float	float	float	float	integer
FEATURES	FeatureNum	Row	Col	Pass	unigene_code	Zone	ProbeUID
ControlType	ProbeName	GeneName	SystematicName	Description	PositionX
PositionY	LogRatio	LogRatioError	PValueLogRatio	gSurrogateUsed
rSurrogateUsed	gIsFound	rIsFound	gProcessedSignal	rProcessedSignal
gProcessedSigError	rProcessedSigError	gNumPixOLHi	rNumPixOLHi
gNumPixOLLo	rNumPixOLLo	gNumPix	rNumPix	gMeanSignal	rMeanSignal
gMedianSignal	rMedianSignal	gPixSDev	rPixSDev	gBGNumPix	rBGNumPix
gBGMeanSignal	rBGMeanSignal	gBGMedianSignal	rBGMedianSignal
gBGPixSDev	rBGPixSDev	gNumSatPix	rNumSatPix	gIsSaturated	rIsSaturated
PixCorrelation	BGPixCorrelation	gIsFeatNonUnifOL	rIsFeatNonUnifOL
gIsBGNonUnifOL	rIsBGNonUnifOL	gIsFeatPopnOL	rIsFeatPopnOL	gIsBGPopnOL
rIsBGPopnOL	IsManualFlag	gBGSubSignal	rBGSubSignal	gBGSubSigError
rBGSubSigError	BGSubSigCorrelation	gIsPosAndSignif	rIsPosAndSignif
gPValFeatEqBG	rPValFeatEqBG	gNumBGUsed	rNumBGUsed	gIsWellAboveBG
rIsWellAboveBG	IsUsedBGAdjust	gBGUsed	rBGUsed	gBGSDUsed	rBGSDUsed
IsNormalization	gDyeNormSignal	rDyeNormSignal	gDyeNormError
rDyeNormError	DyeNormCorrelation	ErrorModel
DATA	1	1	1	-1		1	0	1	Fiducial	Fiducial	Fiducial	Fiducial	32.1844
25.4037	-0.100347	0.0656086	0.126144	0	0	1	1	600.495	476.609	24.0597
18.9299	0	1	0	0	27	27	496	437.593	497	442	31.6617	39.4883	163	163
324.939	248.65	324	243	15.6634	26.3367	0	0	0	0	0.324885
0.000418385	0	0	0	0	0	0	0	0	0	155.132	198.262	6.21557	7.87453
0.307392	1	1	9.66082e-021	1.04613e-021	1	1	1	1	0	340.868	239.331
15.6634	26.3367	0	600.495	476.609	24.0597	18.9299	0.307392	1

Many thanks

-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109
Fax: +44 (0) 20 8722 4141

Email: daniel.brewer at icr.ac.uk

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