Examples with BatchEffectDetails ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails used on opensource projects

Example 1 with BatchEffectDetails

use of ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails in project Gemma by PavlidisLab.

the class GeeqServiceImpl method scoreBatchEffect.

private void scoreBatchEffect(ExpressionExperiment ee, Geeq gq, boolean infoDetected) {
    double score;
    boolean hasInfo = true;
    boolean hasStrong = false;
    boolean hasNone = false;
    boolean corrected = false;
    if (infoDetected) {
        boolean manual = gq.isManualBatchEffectActive();
        if (!manual) {
            BatchEffectDetails be = expressionExperimentService.getBatchEffect(ee);
            if (be == null) {
                Log.warn(this.getClass(), GeeqServiceImpl.ERR_B_EFFECT_BAD_STATE);
                hasInfo = false;
            } else {
                hasStrong = be.getPvalue() < 0.0001;
                hasNone = be.getPvalue() > 0.1;
                corrected = be.getDataWasBatchCorrected();
            }
        } else {
            hasStrong = gq.isManualHasStrongBatchEffect();
            hasNone = gq.isManualHasNoBatchEffect();
        }
    }
    score = !infoDetected || !hasInfo ? GeeqServiceImpl.P_00 : hasStrong ? GeeqServiceImpl.BATCH_EFF_STRONG : hasNone ? GeeqServiceImpl.BATCH_EFF_NONE : GeeqServiceImpl.BATCH_EFF_WEAK;
    gq.setBatchCorrected(corrected);
    gq.setqScoreBatchEffect(score);
}

Example 2 with BatchEffectDetails

use of ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails in project Gemma by PavlidisLab.

the class LinkAnalysisServiceImpl method qcCheck.

/**
 * Reject if experiment has outliers or batch effects.
 */
private void qcCheck(LinkAnalysisConfig config, ExpressionExperiment ee) throws UnsuitableForAnalysisException {
    if (config.isCheckForOutliers()) {
        Collection<OutlierDetails> outliers = outlierDetectionService.identifyOutliersByMedianCorrelation(ee);
        if (!outliers.isEmpty()) {
            throw new UnsuitableForAnalysisException(ee, "Potential outlier samples detected");
        }
    }
    if (config.isCheckForBatchEffect()) {
        BatchEffectDetails batchEffect = eeService.getBatchEffect(ee);
        if (batchEffect.getDataWasBatchCorrected()) {
            LinkAnalysisServiceImpl.log.info("Data are batch-corrected");
            return;
        }
        if (batchEffect.hasNoBatchInfo()) {
            // we may change this behaviour...
            throw new UnsuitableForAnalysisException(ee, "No batch information available, out of an abundance of caution we are skipping");
        }
        if (batchEffect.getPvalue() < 0.001) {
            double componentVarianceProportion = batchEffect.getComponentVarianceProportion();
            Integer component = batchEffect.getComponent();
            // this far.
            if (component > 2 && componentVarianceProportion < 0.1) {
                return;
            }
            throw new UnsuitableForAnalysisException(ee, String.format("Strong batch effect detected (%s)", batchEffect));
        }
    }
}

Example 3 with BatchEffectDetails

use of ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails in project Gemma by PavlidisLab.

the class ExpressionExperimentServiceImpl method getBatchEffect.

@Override
@Transactional(readOnly = true)
public BatchEffectDetails getBatchEffect(ExpressionExperiment ee) {
    ee = this.thawLiter(ee);
    BatchEffectDetails details = new BatchEffectDetails(this.checkHasBatchInfo(ee), this.getHasBeenBatchCorrected(ee));
    if (details.hasNoBatchInfo())
        return details;
    for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) {
        if (BatchInfoPopulationServiceImpl.isBatchFactor(ef)) {
            SVDValueObject svd = svdService.getSvdFactorAnalysis(ee.getId());
            if (svd == null)
                break;
            double minP = 1.0;
            for (Integer component : svd.getFactorPvals().keySet()) {
                Map<Long, Double> cmpEffects = svd.getFactorPvals().get(component);
                Double pVal = cmpEffects.get(ef.getId());
                if (pVal != null && pVal < minP) {
                    details.setPvalue(pVal);
                    details.setComponent(component + 1);
                    details.setComponentVarianceProportion(svd.getVariances()[component]);
                    minP = pVal;
                }
            }
            return details;
        }
    }
    return details;
}

Example 4 with BatchEffectDetails

use of ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails in project Gemma by PavlidisLab.

the class ExpressionExperimentServiceImpl method getBatchEffectDescription.

@Override
@Transactional(readOnly = true)
public String getBatchEffectDescription(ExpressionExperiment ee) {
    BatchEffectDetails beDetails = this.getBatchEffect(ee);
    String result = "";
    if (beDetails == null || beDetails.hasNoBatchInfo()) {
        result = "";
    } else {
        if (beDetails.getDataWasBatchCorrected()) {
            // Checked for in ExpressionExperimentDetails.js::renderStatus()
            result = "Data has been batch-corrected";
        } else if (beDetails.getComponent() != null && beDetails.getPvalue() < ExpressionExperimentServiceImpl.BATCH_EFFECT_THRESHOLD) {
            String pc = beDetails.getComponent() != null ? " (PC " + beDetails.getComponent() + ")" : "";
            result = "This data set may have a batch artifact" + pc + ", p=" + String.format("%.2g", beDetails.getPvalue());
        }
    }
    return Strings.emptyToNull(result);
}