Examples with QuantitationType ubic.gemma.model.common.quantitationtype.QuantitationType used on opensource projects

Example 31 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method getUsefulQuantitationTypes.

/**
 * @param eeQtTypes the QTs
 * @return just the quantitation types that are likely to be 'useful': Preferred, present/absent, signals and background
 * from both channels (if present).
 */
public static Collection<QuantitationType> getUsefulQuantitationTypes(Collection<QuantitationType> eeQtTypes) {
    Collection<QuantitationType> neededQtTypes = new HashSet<>();
    for (QuantitationType qType : eeQtTypes) {
        String name = qType.getName();
        if (qType.getIsPreferred()) {
            ExpressionDataMatrixBuilder.log.info("Preferred=" + qType);
            neededQtTypes.add(qType);
        } else if (qType.getIsMaskedPreferred()) {
            ExpressionDataMatrixBuilder.log.info("Masked preferred=" + qType);
            neededQtTypes.add(qType);
        } else if (ChannelUtils.isBackgroundChannelA(name)) {
            neededQtTypes.add(qType);
            ExpressionDataMatrixBuilder.log.info("Background A=" + qType);
        } else if (ChannelUtils.isBackgroundChannelB(name)) {
            neededQtTypes.add(qType);
            ExpressionDataMatrixBuilder.log.info("Background B=" + qType);
        } else if (ChannelUtils.isSignalChannelA(name)) {
            neededQtTypes.add(qType);
            ExpressionDataMatrixBuilder.log.info("Signal A=" + qType);
        } else if (ChannelUtils.isSignalChannelB(name)) {
            neededQtTypes.add(qType);
            ExpressionDataMatrixBuilder.log.info("Signal B=" + qType);
        } else if (name.matches("CH1D_MEAN")) {
            /*
                 * Special case. This is the background subtracted channel 1 for GenePix data. It is only needed to
                 * reconstruct CH1 if it isn't present, which is surprisingly common in Stanford data sets
                 */
            neededQtTypes.add(qType);
        } else if (qType.getType().equals(StandardQuantitationType.PRESENTABSENT)) {
            ExpressionDataMatrixBuilder.log.info("Present/absent=" + qType);
            neededQtTypes.add(qType);
        }
    }
    return neededQtTypes;
}

Example 32 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method isTwoColor.

private boolean isTwoColor() {
    for (DesignElementDataVector v : vectors) {
        CompositeSequence d = v.getDesignElement();
        TechnologyType technologyType = d.getArrayDesign().getTechnologyType();
        if (technologyType.equals(TechnologyType.ONECOLOR) || technologyType.equals(TechnologyType.NONE)) {
            continue;
        }
        QuantitationType qt = v.getQuantitationType();
        if ((qt.getIsPreferred() || qt.getIsMaskedPreferred()) && qt.getIsRatio()) {
            return true;
        }
    }
    return false;
}

Example 33 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method getBkgSubChannelA.

public ExpressionDataDoubleMatrix getBkgSubChannelA() {
    if (dat == null)
        dat = this.getQuantitationTypesNeeded();
    List<BioAssayDimension> dimensions = this.getBioAssayDimensions();
    List<QuantitationType> qTypes = new ArrayList<>();
    for (BioAssayDimension dimension : dimensions) {
        QuantitationType qType = dat.getBkgSubChannelA(dimension);
        if (qType != null)
            qTypes.add(qType);
    }
    if (qTypes.size() != 0) {
        return this.makeMatrix(qTypes);
    }
    return null;
}

Example 34 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method getBackgroundChannelA.

public ExpressionDataDoubleMatrix getBackgroundChannelA() {
    if (dat == null)
        dat = this.getQuantitationTypesNeeded();
    List<BioAssayDimension> dimensions = this.getBioAssayDimensions();
    List<QuantitationType> qTypes = new ArrayList<>();
    for (BioAssayDimension dimension : dimensions) {
        QuantitationType qType = dat.getBackgroundChannelA(dimension);
        if (qType != null)
            qTypes.add(qType);
    }
    if (qTypes.size() != 0) {
        return this.makeMatrix(qTypes);
    }
    return null;
}

Example 35 with QuantitationType

use of ubic.gemma.model.common.quantitationtype.QuantitationType in project Gemma by PavlidisLab.

the class QuantitationTypeData method getBackgroundChannelB.

public ExpressionDataDoubleMatrix getBackgroundChannelB() {
    if (dat == null)
        dat = this.getQuantitationTypesNeeded();
    List<BioAssayDimension> dimensions = this.getBioAssayDimensions();
    List<QuantitationType> qTypes = new ArrayList<>();
    for (BioAssayDimension dimension : dimensions) {
        QuantitationType qType = dat.getBackgroundChannelB(dimension);
        if (qType != null)
            qTypes.add(qType);
    }
    if (qTypes.size() != 0) {
        return this.makeMatrix(qTypes);
    }
    return null;
}