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

Example 56 with ExpressionExperiment

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

the class GeoConverterTest method testConvertMultiSeriesPerSample.

/*
     * Case where the same sample can be in multiple series, we had problems with it.
     */
@Test
public void testConvertMultiSeriesPerSample() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE3193Short/GSE3193_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE3193");
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment ee = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    // assertEquals( 85, ee.getBioAssays().size() );
    Map<ArrayDesign, Integer> ads = new HashMap<>();
    for (BioAssay b : ee.getBioAssays()) {
        if (ads.containsKey(b.getArrayDesignUsed())) {
            ads.put(b.getArrayDesignUsed(), ads.get(b.getArrayDesignUsed()) + 1);
        } else {
            ads.put(b.getArrayDesignUsed(), 1);
        }
    }
    assertEquals(4, ads.size());
    for (ArrayDesign ad : ads.keySet()) {
        Integer count = ads.get(ad);
        switch(ad.getName()) {
            case "SHAC":
                // ok
                assertEquals(8, count.intValue());
                break;
            case "SVJ":
                // ok
                assertEquals(1, count.intValue());
                break;
            case "SVL_SVM_SVN_SVO":
                assertEquals(32, count.intValue());
                break;
            case "SVC":
                assertEquals(44, count.intValue());
                break;
            default:
                fail("Name was " + ad.getName());
                break;
        }
    }
}

Example 57 with ExpressionExperiment

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

the class GeoConverterTest method testConvertGse59.

@SuppressWarnings("unchecked")
@Test
public void testConvertGse59() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE59Short/GSE59_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE59");
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    // GeoValues values = series.getValues();
    // System.err.print( values );
    Object result = this.gc.convert(series);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    ExpressionExperiment ee = ees.iterator().next();
    boolean ok = this.checkQts(ee);
    assertTrue(ok);
}

Example 58 with ExpressionExperiment

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

the class GeoConverterTest method testGSE8872.

/*
     * Has only one GDS in GEOs when there really should be two. Bug 1829.
     */
@SuppressWarnings("unchecked")
@Test
public final void testGSE8872() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse8872short/GSE8872_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse8872short/GDS2942.soft.gz"));
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE8872");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    assertEquals(1, ees.size());
}

Example 59 with ExpressionExperiment

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

the class GeoConverterTest method testParseGSE44625.

/*
     * bug 3415. The samples do not have the same quantitation types. In some it is "detection pval" and others
     * "raw_value". We would reject "detection pval" but if the qt already has the name "raw_value" we won't. The way
     * the current setup works, we sort of throw up our hands and keep the data, even though it is messed up.
     * <p>
     * This tests that behaviour. If we start rejecting the data, this test will fail (note that rejecting the data is
     * not unreasonable).
     */
@Test
public void testParseGSE44625() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE44625.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoParseResult result = (GeoParseResult) parser.getResults().iterator().next();
    GeoSeries series = result.getSeries().values().iterator().next();
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object convert = this.gc.convert(series);
    ExpressionExperiment ee = (ExpressionExperiment) ((Collection<?>) convert).iterator().next();
    assertEquals(2, ee.getQuantitationTypes().size());
}

Example 60 with ExpressionExperiment

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

the class GeoConverterTest method testConvertGSE2122SAGE.

// No SAGE allowed
@SuppressWarnings("unchecked")
@Test
public void testConvertGSE2122SAGE() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse2122shortSage/GSE2122.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2122");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    // SAGE, rejected
    assertEquals(0, ees.size());
}