Examples with BioMaterial ubic.gemma.model.expression.biomaterial.BioMaterial used on opensource projects

Example 71 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class SVDServiceHelperImpl method getFactorsForAnalysis.

private void getFactorsForAnalysis(Collection<BioAssay> bioAssays, Map<Long, Date> bioMaterialDates, Map<ExperimentalFactor, Map<Long, Double>> bioMaterialFactorMap) {
    for (BioAssay bioAssay : bioAssays) {
        Date processingDate = bioAssay.getProcessingDate();
        BioMaterial bm = bioAssay.getSampleUsed();
        // can be null
        bioMaterialDates.put(bm.getId(), processingDate);
        SVDServiceHelperImpl.populateBMFMap(bioMaterialFactorMap, bm);
    }
}

Example 72 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class BatchConfound method getBioMaterialFactorMap.

private static Map<ExperimentalFactor, Map<Long, Double>> getBioMaterialFactorMap(ExpressionExperiment ee) {
    Map<ExperimentalFactor, Map<Long, Double>> bioMaterialFactorMap = new HashMap<>();
    for (BioAssay bioAssay : ee.getBioAssays()) {
        BioMaterial bm = bioAssay.getSampleUsed();
        SVDServiceHelperImpl.populateBMFMap(bioMaterialFactorMap, bm);
    }
    return bioMaterialFactorMap;
}

Example 73 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class ExpressionExperimentBatchCorrectionServiceImpl method checkCorrectability.

@Override
public boolean checkCorrectability(ExpressionExperiment ee, boolean force) {
    for (QuantitationType qt : expressionExperimentService.getQuantitationTypes(ee)) {
        if (qt.getIsBatchCorrected()) {
            ExpressionExperimentBatchCorrectionServiceImpl.log.warn("Experiment already has a batch-corrected quantitation type: " + ee + ": " + qt);
            return false;
        }
    }
    ExperimentalFactor batch = this.getBatchFactor(ee);
    if (batch == null) {
        ExpressionExperimentBatchCorrectionServiceImpl.log.warn("No batch factor found: " + ee);
        return false;
    }
    String bConf = expressionExperimentService.getBatchConfound(ee);
    if (bConf != null && !force) {
        ExpressionExperimentBatchCorrectionServiceImpl.log.warn("Experiment can not be batch corrected: " + bConf);
        ExpressionExperimentBatchCorrectionServiceImpl.log.info("To force batch-correction of a confounded experiment, use the force option (note, that this option also allows outliers while batch correcting).");
        return false;
    }
    /*
         * Make sure we have at least two samples per batch. This generally won't happen if batches were defined by
         * Gemma.
         */
    Map<Long, Integer> batches = new HashMap<>();
    Set<BioMaterial> seen = new HashSet<>();
    for (BioAssay ba : ee.getBioAssays()) {
        BioMaterial bm = ba.getSampleUsed();
        if (seen.contains(bm))
            continue;
        seen.add(bm);
        for (FactorValue fv : bm.getFactorValues()) {
            if (fv.getExperimentalFactor().equals(batch)) {
                Long batchId = fv.getId();
                if (!batches.containsKey(batchId))
                    batches.put(batchId, 0);
                batches.put(batchId, batches.get(batchId) + 1);
            }
        }
    }
    /*
         * consider merging batches. - we already do this when we create the batch factor, so in general batches should
         * always have at least 2 samples
         */
    for (Long batchId : batches.keySet()) {
        if (batches.get(batchId) < 2) {
            ExpressionExperimentBatchCorrectionServiceImpl.log.info("Batch with only one sample detected, correction not possible: " + ee + ", batchId=" + batchId);
            return false;
        }
    }
    return true;
}

Example 74 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class ExpressionExperimentBatchCorrectionServiceImpl method doComBat.

private ExpressionDataDoubleMatrix doComBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix, ObjectMatrix<BioMaterial, ExperimentalFactor, Object> design) {
    ObjectMatrix<BioMaterial, String, Object> designU = this.convertFactorValuesToStrings(design);
    DoubleMatrix<CompositeSequence, BioMaterial> matrix = originalDataMatrix.getMatrix();
    designU = this.orderMatrix(matrix, designU);
    ScaleType scale = originalDataMatrix.getQuantitationTypes().iterator().next().getScale();
    boolean transformed = false;
    if (!(scale.equals(ScaleType.LOG2) || scale.equals(ScaleType.LOG10) || scale.equals(ScaleType.LOGBASEUNKNOWN) || scale.equals(ScaleType.LN))) {
        ExpressionExperimentBatchCorrectionServiceImpl.log.info(" *** COMBAT: LOG TRANSFORMING ***");
        transformed = true;
        MatrixStats.logTransform(matrix);
    }
    /*
         * Process
         */
    ComBat<CompositeSequence, BioMaterial> comBat = new ComBat<>(matrix, designU);
    // false: NONPARAMETRIC
    DoubleMatrix2D results = comBat.run(true);
    // note these plots always reflect the parametric setup.
    // TEMPORARY?
    comBat.plot(ee.getId() + "." + FileTools.cleanForFileName(ee.getShortName()));
    /*
         * Postprocess. Results is a raw matrix/
         */
    DoubleMatrix<CompositeSequence, BioMaterial> correctedDataMatrix = new DenseDoubleMatrix<>(results.toArray());
    correctedDataMatrix.setRowNames(matrix.getRowNames());
    correctedDataMatrix.setColumnNames(matrix.getColNames());
    if (transformed) {
        MatrixStats.unLogTransform(correctedDataMatrix);
    }
    ExpressionDataDoubleMatrix correctedExpressionDataMatrix = new ExpressionDataDoubleMatrix(originalDataMatrix, correctedDataMatrix);
    assert correctedExpressionDataMatrix.getQuantitationTypes().size() == 1;
    /*
         * It is easier if we make a new quantitationtype.
         */
    QuantitationType oldQt = correctedExpressionDataMatrix.getQuantitationTypes().iterator().next();
    QuantitationType newQt = this.makeNewQuantitationType(oldQt);
    correctedExpressionDataMatrix.getQuantitationTypes().clear();
    correctedExpressionDataMatrix.getQuantitationTypes().add(newQt);
    // Sanity check...
    for (int i = 0; i < correctedExpressionDataMatrix.columns(); i++) {
        assert correctedExpressionDataMatrix.getBioMaterialForColumn(i).equals(originalDataMatrix.getBioMaterialForColumn(i));
    }
    return correctedExpressionDataMatrix;
}

Example 75 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class ExpressionExperimentBatchCorrectionServiceImpl method comBat.

@Override
public ExpressionDataDoubleMatrix comBat(ExpressionDataDoubleMatrix originalDataMatrix) {
    ExpressionExperiment ee = originalDataMatrix.getExpressionExperiment();
    ee = expressionExperimentService.thawLite(ee);
    /*
         * is there a batch to use?
         */
    ExperimentalFactor batch = this.getBatchFactor(ee);
    if (batch == null) {
        ExpressionExperimentBatchCorrectionServiceImpl.log.warn("No batch factor found");
        return null;
    }
    ObjectMatrix<BioMaterial, ExperimentalFactor, Object> design = this.getDesign(ee, originalDataMatrix);
    return this.doComBat(ee, originalDataMatrix, design);
}