Class ExpressionDataMatrixBuilder


  • public class ExpressionDataMatrixBuilder
    extends Object
    Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc. This class is not database aware; use the ExpressionDataMatrixService to get ready-to-use matrices starting from an ExpressionExperiment. This handles complexities such as experiments that contain multiple array designs with differing quantitation types.
    Author:
    pavlidis
    • Method Detail

      • getMatrix

        public static ExpressionDataMatrix<?> getMatrix​(Collection<? extends DesignElementDataVector> vectors)
        Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.
        Parameters:
        vectors - raw vectors
        Returns:
        matrix of appropriate type.
      • getMissingValueQuantitationTypes

        public static Collection<QuantitationType> getMissingValueQuantitationTypes​(ExpressionExperiment expressionExperiment)
        Parameters:
        expressionExperiment - (should be lightly thawed)
        Returns:
        a collection of QTs
      • getUsefulQuantitationTypes

        public static Collection<QuantitationType> getUsefulQuantitationTypes​(Collection<QuantitationType> eeQtTypes)
        Parameters:
        eeQtTypes - the QTs
        Returns:
        just the quantitation types that are likely to be 'useful': Preferred, present/absent, signals and background from both channels (if present).
      • getUsefulQuantitationTypes

        public static Collection<QuantitationType> getUsefulQuantitationTypes​(ExpressionExperiment expressionExperiment)
        Parameters:
        expressionExperiment - the EE to get the QTs for
        Returns:
        just the quantitation types that are likely to be 'useful': Preferred, present/absent, signals and background from both channels (if present).
      • getBioAssayDimensions

        public List<BioAssayDimension> getBioAssayDimensions()
        Returns:
        a single BioAssayDimension except if there are multiple array designs used in the experiment.
      • getIntensity

        public ExpressionDataDoubleMatrix getIntensity()
        Returns:
        Compute an intensity matrix. For two-channel arrays, this is the geometric mean of the background-subtracted signals on the two channels. For two-color arrays, if one channel is missing (as happens sometimes) the intensities returned are just from the one channel. For one-color arrays, this is the same as the preferred data matrix.
      • getMissingValueData

        public ExpressionDataBooleanMatrix getMissingValueData()
        Returns:
        a matrix of booleans, or null if a missing value quantitation type ("absent/present", which may have been computed by our system) is not found. This will return the values whether the array design is two-color or not.
      • getPreferredData

        public ExpressionDataDoubleMatrix getPreferredData()
        Returns:
        The matrix for the preferred data - NOT the processed data (though they may be the same, in fact)
      • isAnyMissing

        public boolean isAnyMissing()