[BioC] Format identification

lgautier at altern.org lgautier at altern.org
Wed Jan 3 14:17:03 CET 2007 

The string "AGILENT_SCANNER" (3rd line) seems to point in the direction of
an Agilent array.


HTH,


Laurent



> 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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