broad.pda.geneexpression.agilent.AgilentUtils Class Reference

Static Public Member Functions
static Map< String, AgilentProbe >	parseAgilentExperiment (File file) throws IOException
static AgilentArrayStats	parseAgilentExperimentGlobalStats (File file) throws IOException
static Map< String, ExpressionExperimentInfo >	parseExperimentInfoFile (File experimentInfoFile) throws IOException
static Map< String, String >	parseExperimentInfoFileToName (File experimentInfoFile) throws IOException
static Map< String, String >	parseExperimentInfoFileToName (File experimentInfoFile, boolean passingFilter) throws IOException
static Map< String, Collection < ExpressionExperimentInfo > >	parseExperimentInfoFileToGroup (File experimentInfoFile) throws IOException
static Map< String, Collection < String > >	parseExperimentInfoFileToGroups (File experimentInfoFile) throws IOException
static Map< String, Double >	makeDataMatrix (File agilentFile, Collection< String > nonFlaggedGenes) throws IOException
static MatrixWithHeaders	makeDataMatrix (File[] agilentFiles) throws IOException
static MatrixWithHeaders	makeDataMatrix (File[] agilentFiles, Map< String, ExpressionExperimentInfo > experimentInfo) throws IOException
static Map< String, Collection < String > >	parseExperimentInfoGroups (String experimentInfoFile) throws IOException
static Map< String, Collection < String > >	parseExperimentInfoNonControls (String experimentInfoFile) throws IOException
static Collection< String >	parseControlSamples (String experimentInfoFile) throws IOException

Member Function Documentation

static Map<String, Double> broad.pda.geneexpression.agilent.AgilentUtils.makeDataMatrix ( File  agilentFile, Collection< String >  nonFlaggedGenes  ) throws IOException

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static MatrixWithHeaders broad.pda.geneexpression.agilent.AgilentUtils.makeDataMatrix ( File[]  agilentFiles ) throws IOException

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static MatrixWithHeaders broad.pda.geneexpression.agilent.AgilentUtils.makeDataMatrix ( File[]  agilentFiles, Map< String, ExpressionExperimentInfo >  experimentInfo  ) throws IOException

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static Map<String, AgilentProbe> broad.pda.geneexpression.agilent.AgilentUtils.parseAgilentExperiment ( File  file ) throws IOException

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static AgilentArrayStats broad.pda.geneexpression.agilent.AgilentUtils.parseAgilentExperimentGlobalStats ( File  file ) throws IOException

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static Collection<String> broad.pda.geneexpression.agilent.AgilentUtils.parseControlSamples ( String  experimentInfoFile ) throws IOException

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static Map<String, ExpressionExperimentInfo> broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoFile ( File  experimentInfoFile ) throws IOException

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static Map<String, Collection<ExpressionExperimentInfo> > broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoFileToGroup ( File  experimentInfoFile ) throws IOException

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static Map<String, Collection<String> > broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoFileToGroups ( File  experimentInfoFile ) throws IOException

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static Map<String, String> broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoFileToName ( File  experimentInfoFile ) throws IOException

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static Map<String, String> broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoFileToName ( File  experimentInfoFile, boolean  passingFilter  ) throws IOException

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static Map<String, Collection<String> > broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoGroups ( String  experimentInfoFile ) throws IOException

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static Map<String, Collection<String> > broad.pda.geneexpression.agilent.AgilentUtils.parseExperimentInfoNonControls ( String  experimentInfoFile ) throws IOException

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The documentation for this class was generated from the following file:

• java/broad/pda/geneexpression/agilent/AgilentUtils.java