Examples with ExpressionExperiment ubic.gemma.model.expression.experiment.ExpressionExperiment used on opensource projects

Example 26 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class CompositeSequenceGeneMapperServiceTest method cleanup.

@After
public void cleanup() {
    ad = arrayDesignService.findByShortName(arrayAccession);
    if (ad != null) {
        for (ExpressionExperiment ee : arrayDesignService.getExpressionExperiments(ad)) {
            eeService.remove(ee);
        }
        arrayDesignService.remove(ad);
    }
    Collection<Gene> genes = geneService.loadAll();
    for (Gene gene : genes) {
        try {
            geneService.remove(gene);
        } catch (Exception ignored) {
        }
    }
}

Example 27 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class ExpressionDataDoubleMatrixTest method testMatrixConversion.

@Test
public void testMatrixConversion() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("")));
        Collection<?> results = geoService.fetchAndLoad("GSE8294", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    newee = expressionExperimentService.thaw(newee);
    // make sure we really thawRawAndProcessed them, so we can get the design element sequences.
    Collection<RawExpressionDataVector> vectors = newee.getRawExpressionDataVectors();
    rawExpressionDataVectorService.thaw(vectors);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(vectors);
    ExpressionDataDoubleMatrix matrix = builder.getPreferredData();
    assertTrue(!Double.isNaN(matrix.get(10, 0)));
    assertEquals(66, matrix.rows());
    assertEquals(9, matrix.columns());
    /*
         * Additional tests for files and outlier marking.
         */
    processedDataVectorService.computeProcessedExpressionData(newee);
    File f1 = expressionDataFileService.writeOrLocateDataFile(expressionExperimentService.load(newee.getId()), true, true);
    assertNotNull(f1);
    assertTrue(f1.exists());
    expressionDataFileService.deleteAllFiles(newee);
    assertTrue(!f1.exists());
    /*
         * outlier removal.
         */
    BioAssay tba = newee.getBioAssays().iterator().next();
    Collection<BioAssay> ol = new HashSet<>();
    ol.add(tba);
    sampleRemoveService.markAsMissing(ol);
    assertTrue(tba.getIsOutlier());
    newee = expressionExperimentService.thaw(newee);
    Collection<ProcessedExpressionDataVector> vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    ExpressionDataMatrixBuilder matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    ExpressionDataDoubleMatrix data = matrixBuilder.getProcessedData();
    assertNotNull(data);
    assertTrue(Double.isNaN(data.getColumn(tba)[10]));
    sampleRemoveService.unmarkAsMissing(ol);
    newee = expressionExperimentService.load(newee.getId());
    newee = expressionExperimentService.thaw(newee);
    vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    data = matrixBuilder.getProcessedData();
    assertTrue(!tba.getIsOutlier());
    assertTrue(!Double.isNaN(data.getColumn(tba)[10]));
}

Example 28 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class DataUpdaterTest method tearDown.

@After
public void tearDown() {
    ExpressionExperiment e1 = experimentService.findByShortName("GSE29006");
    if (e1 != null) {
        experimentService.remove(e1);
    }
    ExpressionExperiment e2 = experimentService.findByShortName("GSE19166");
    if (e2 != null) {
        experimentService.remove(e2);
    }
    ExpressionExperiment e3 = experimentService.findByShortName("GSE37646");
    if (e3 != null) {
        experimentService.remove(e3);
    }
    if (targetArrayDesign != null)
        arrayDesignService.remove(targetArrayDesign);
}

Example 29 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class DataUpdaterTest method testAddData.

@Test
public void testAddData() throws Exception {
    /*
         * Load a regular data set that has no data. Platform is (basically) irrelevant.
         */
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
    ExpressionExperiment ee;
    try {
        // RNA-seq data.
        Collection<?> results = geoService.fetchAndLoad("GSE37646", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // log.warn( "Test skipped because GSE37646 was not removed from the system prior to test" );
        ee = (ExpressionExperiment) ((List<?>) e.getData()).get(0);
    }
    ee = experimentService.thawLite(ee);
    List<BioAssay> bioAssays = new ArrayList<>(ee.getBioAssays());
    assertEquals(31, bioAssays.size());
    List<BioMaterial> bms = new ArrayList<>();
    for (BioAssay ba : bioAssays) {
        bms.add(ba.getSampleUsed());
    }
    targetArrayDesign = this.getTestPersistentArrayDesign(100, true);
    DoubleMatrix<CompositeSequence, BioMaterial> rawMatrix = new DenseDoubleMatrix<>(targetArrayDesign.getCompositeSequences().size(), bms.size());
    /*
         * make up some fake data on another platform, and match it to those samples
         */
    for (int i = 0; i < rawMatrix.rows(); i++) {
        for (int j = 0; j < rawMatrix.columns(); j++) {
            rawMatrix.set(i, j, (i + 1) * (j + 1) * Math.random() / 100.0);
        }
    }
    List<CompositeSequence> probes = new ArrayList<>(targetArrayDesign.getCompositeSequences());
    rawMatrix.setRowNames(probes);
    rawMatrix.setColumnNames(bms);
    QuantitationType qt = this.makeQt(true);
    ExpressionDataDoubleMatrix data = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    assertNotNull(data.getBestBioAssayDimension());
    assertEquals(rawMatrix.columns(), data.getBestBioAssayDimension().getBioAssays().size());
    assertEquals(probes.size(), data.getMatrix().rows());
    /*
         * Replace it.
         */
    ee = dataUpdater.replaceData(ee, targetArrayDesign, data);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    ee = experimentService.thaw(ee);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    assertEquals(100, ee.getRawExpressionDataVectors().size());
    for (RawExpressionDataVector v : ee.getRawExpressionDataVectors()) {
        assertTrue(v.getQuantitationType().getIsPreferred());
    }
    assertEquals(100, ee.getProcessedExpressionDataVectors().size());
    Collection<DoubleVectorValueObject> processedDataArrays = dataVectorService.getProcessedDataArrays(ee);
    for (DoubleVectorValueObject v : processedDataArrays) {
        assertEquals(31, v.getBioAssays().size());
    }
    /*
         * Test adding data (non-preferred)
         */
    qt = this.makeQt(false);
    ExpressionDataDoubleMatrix moreData = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    ee = dataUpdater.addData(ee, targetArrayDesign, moreData);
    ee = experimentService.thaw(ee);
    try {
        // add preferred data twice.
        dataUpdater.addData(ee, targetArrayDesign, data);
        fail("Should have gotten an exception");
    } catch (IllegalArgumentException e) {
    // okay.
    }
    dataUpdater.deleteData(ee, qt);
}

Example 30 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class DataUpdaterTest method testLoadRNASeqDataWithMissingSamples.

/*
     * Test case where some samples cannot be used.
     *
     */
@Test
public void testLoadRNASeqDataWithMissingSamples() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGenerator());
    ExpressionExperiment ee = experimentService.findByShortName("GSE29006");
    if (ee != null) {
        experimentService.remove(ee);
    }
    assertTrue(experimentService.findByShortName("GSE29006") == null);
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE29006", false, false, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        throw new IllegalStateException("Need to remove this data set before test is run");
    }
    ee = experimentService.thaw(ee);
    // Load the data from a text file.
    DoubleMatrixReader reader = new DoubleMatrixReader();
    try (InputStream countData = this.getClass().getResourceAsStream("/data/loader/expression/flatfileload/GSE29006_expression_count.test.txt");
        InputStream rpkmData = this.getClass().getResourceAsStream("/data/loader/expression/flatfileload/GSE29006_expression_RPKM.test.txt")) {
        DoubleMatrix<String, String> countMatrix = reader.read(countData);
        DoubleMatrix<String, String> rpkmMatrix = reader.read(rpkmData);
        List<String> probeNames = countMatrix.getRowNames();
        // we have to find the right generic platform to use.
        targetArrayDesign = this.getTestPersistentArrayDesign(probeNames, taxonService.findByCommonName("human"));
        targetArrayDesign = arrayDesignService.thaw(targetArrayDesign);
        try {
            dataUpdater.addCountData(ee, targetArrayDesign, countMatrix, rpkmMatrix, 36, true, false);
            fail("Should have gotten an exception");
        } catch (IllegalArgumentException e) {
        // Expected
        }
        dataUpdater.addCountData(ee, targetArrayDesign, countMatrix, rpkmMatrix, 36, true, true);
    }
    /*
         * Check
         */
    ee = experimentService.thaw(ee);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    ExpressionDataDoubleMatrix mat = dataMatrixService.getProcessedExpressionDataMatrix(ee);
    assertEquals(199, mat.rows());
    assertTrue(mat.getQuantitationTypes().iterator().next().getName().startsWith("log2cpm"));
    assertEquals(4, ee.getBioAssays().size());
    assertEquals(199 * 3, ee.getRawExpressionDataVectors().size());
    assertEquals(199, ee.getProcessedExpressionDataVectors().size());
    Collection<DoubleVectorValueObject> processedDataArrays = dataVectorService.getProcessedDataArrays(ee);
    assertEquals(199, processedDataArrays.size());
    TestUtils.assertBAs(ee, targetArrayDesign, "GSM718709", 320383);
    for (DoubleVectorValueObject v : processedDataArrays) {
        assertEquals(4, v.getBioAssays().size());
    }
}