Hi there,
I've configured a plugin for agilent raw import:
blockColumnMapping FeatureNum
columnColumnMapping Column
dataFooterRegexp
dataHeaderRegexp ^FEATURES\tFeatureNum\tRow\tCol\tchr_coord\taccessions\tProbeUID\tControlType\tProbeName\tGeneName\tSystematicName\tDescription\tPositionX\tPositionY\tLogRatio\tLogRatioError\tPValueLogRatio\tgSurrogateUsed\trSurrogateUsed\tgIsFound\trIsFound\tgProcessedSignal\trProcessedSignal\tgProcessedSigError\trProcessedSigError\tgNumPixOLHi\trNumPixOLHi\tgNumPixOLLo\trNumPixOLLo\tgNumPix\trNumP ix\tgMeanSignal\trMeanSignal\tgMedianSignal\trMedianSignal\tgPixSDev\trPixSDev\tgBGNumPix\trBGNumPix\tgBGMeanSignal\trBGMeanSignal\tgBGMedianSignal\trBGMedianSignal\tgBGPixSDev\trBGPixSDev\tgNumSatPix\trNumSatPix\tgIsSaturated\trIsSaturated\tPixCorrelation\ tBGPixCorrelation\tgIsFeatNonUnifOL\trIsFeatNonUnifOL\tgIsBGNonUnifOL\trIsBGNonUnifOL\tgIsFeatPopnOL\trIsFeatPopnOL\tgIsBGPopnOL\trIsBGPopnOL\tIsManualFlag\tgBGSubSignal\trBGSubSignal\tgBGSubSigError\trBGSubSigError\tBGSubSigCorrelation\tgIsPosAndSignif\t rIsPosAndSignif\tgPValFeatEqBG\trPValFeatEqBG\tgNumBGUsed\trNumBGUsed\tgIsWellAboveBG\trIsWellAboveBG\tgBGUsed\trBGUsed\tgBGSDUsed\trBGSDUsed\tIsNormalization\tgDyeNormSignal\trDyeNormSignal\tgDyeNormError\trDyeNormError\tDyeNormCorrelation\tErrorModel\txD ev\tgSpatialDetrendIsInFilteredSet\trSpatialDetrendIsInFilteredSet\tgSpatialDetrendSurfaceValue\trSpatialDetrendSurfaceValue
dataSplitterRegexp \t
headerRegexp
ignoreRegexp
maxDataColumns
metaGridXColumnMapping
metaGridYColumnMapping
minDataColumns
propertyMapping.BGPixCorrelation BGPixCorrelation
propertyMapping.BGSubSigCorrelation BGSubSigCorrelation
propertyMapping.DyeNormCorrelation DyeNormCorrelation
propertyMapping.ErrorModel ErrorModel
propertyMapping.IsManualFlag IsManualFlag
propertyMapping.IsNormalization IsNormalization
propertyMapping.LogRatio LogRatio
propertyMapping.PValueLogRatio PValueLogRatio
propertyMapping.PixCorrelation PixCorrelation
propertyMapping.gBGMeanSignal gBGMeanSignal
propertyMapping.gBGMedianSignal gBGMedianSignal
propertyMapping.gBGNumPix gBGNumPix
propertyMapping.gBGSubSignal gBGSubSignal
propertyMapping.gBGUsed gBGUsed
propertyMapping.gDyeNormSignal gDyeNormSignal
propertyMapping.gIsBGNonUnifOL gIsBGNonUnifOL
propertyMapping.gIsBGPopnOL gIsBGPopnOL
propertyMapping.gIsFeatNonUnifOL gIsFeatNonUnifOL
propertyMapping.gIsFeatPopnOL gIsFeatPopnOL
propertyMapping.gIsFound gIsFound
propertyMapping.gIsPosAndSignif gIsPosAndSignif
propertyMapping.gIsSaturated gIsSaturated
propertyMapping.gIsWellAboveBG gIsWellAboveBG
propertyMapping.gMeanSignal gMeanSignal
propertyMapping.gMedianSignal gMedianSignal
propertyMapping.gNumBGUsed gNumBGUsed
propertyMapping.gNumPix gNumPix
propertyMapping.gNumPixOLHi gNumPixOLHi
propertyMapping.gNumPixOLLo gNumPixOLLo
propertyMapping.gNumSatPix gNumSatPix
propertyMapping.gPValFeatEqBG gPValFeatEqBG
propertyMapping.gProcessedSignal gProcessedSignal
propertyMapping.gSpatialDetrendIsInFilteredSet gSpatialDetrendIsInFilteredSet
propertyMapping.gSpatialDetrendSurfaceValue gSpatialDetrendSurfaceValue
propertyMapping.gSurrogateUsed gSurrogateUsed
propertyMapping.rBGMeanSignal rBGMeanSignal
propertyMapping.rBGMedianSignal rBGMedianSignal
propertyMapping.rBGNumPix rBGNumPix
propertyMapping.rBGSubSignal rBGSubSignal
propertyMapping.rBGUsed rBGUsed
propertyMapping.rDyeNormSignal rDyeNormSignal
propertyMapping.rIsBGNonUnifOL rIsBGNonUnifOL
propertyMapping.rIsBGPopnOL rIsBGPopnOL
propertyMapping.rIsFeatNonUnifOL rIsFeatNonUnifOL
propertyMapping.rIsFeatPopnOL rIsFeatPopnOL
propertyMapping.rIsFound rIsFound
propertyMapping.rIsPosAndSignif rIsPosAndSignif
propertyMapping.rIsSaturated rIsSaturated
propertyMapping.rIsWellAboveBG rIsWellAboveBG
propertyMapping.rMeanSignal rMeanSignal
propertyMapping.rMedianSignal rMedianSignal
propertyMapping.rNumBGUsed rNumBGUsed
propertyMapping.rNumPix rNumPix
propertyMapping.rNumPixOLHi rNumPixOLHi
propertyMapping.rNumPixOLLo rNumPixOLLo
propertyMapping.rNumSatPix rNumSatPix
propertyMapping.rPValFeatEqBG rPValFeatEqBG
propertyMapping.rProcessedSignal rProcessedSignal
propertyMapping.rSpatialDetrendIsInFilteredSet rSpatialDetrendIsInFilteredSet
propertyMapping.rSpatialDetrendSurfaceValue rSpatialDetrendSurfaceValue
propertyMapping.rSurrogateUsed rSurrogateUsed
propertyMapping.xDev xDev
rawDataType agilent
reporterIdColumnMapping ProbeName
rowColumnMapping Row
trimQuotes true
xColumnMapping
yColumnMapping
But when I import a typical Agilent Feature Extraction output raw file, I got an import error showing below. (data starts on line11, and line10 is Data header).
Please help, thanks very much!
David
View job -- Import raw bioassay
Name Import raw bioassay
Description
Priority 4 (1 = highest, 10 = lowest)
Status Error: Import failed on line 11: For input string: "LogRatio"
BaseException: Import failed on line 11: For input string: "LogRatio"
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:399)
at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:312)
at PluginExecutionRequest.invoke(PluginExecutionRequest.java:84)
at InternalJobQueue$JobRunner.run(InternalJobQueue.java:445)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NumberFormatException: For input string: "LogRatio"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224)
at java.lang.Float.valueOf(Float.java:360)
at java.lang.Float.<init>(Float.java:461)
at org.hibernate.type.FloatType.fromStringValue(FloatType.java:51)
at Type.parseString(Type.java:357)
at ExtendedProperty.parseString(ExtendedProperty.java:153)
at net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFileImporter.java:411)
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:395)
... 4 more
Percent complete
100%
Created 2006-05-24 09:15
Started 2006-05-24 09:15
Ended 2006-05-24 09:15
Server lin2.activx.com
Plugin Text file raw data importer
Configuration agilent raw data
file /home/US22502657_251197832125_S01_A01.txt
rawBioAssay R3_20050822
