Package ubic.gemma.core.analysis.preprocess.batcheffects

Interface ExpressionExperimentBatchInformationService

All Known Implementing Classes:

ExpressionExperimentBatchInformationServiceImpl

public interface ExpressionExperimentBatchInformationService

Provides status of batch information for datasets.

Method Summary

Modifier and Type	Method	Description
boolean	checkHasBatchInfo(ExpressionExperiment ee)	Check if the given experiment has batch information.
boolean	checkHasUsableBatchInfo(ExpressionExperiment ee)	Check if the given experiment has usable batch information.
String	getBatchConfoundAsHtmlString(ExpressionExperiment ee)	Summarize the batch confounds for a given dataset or its subsets in an HTML string.
BatchEffectType	getBatchEffect(ExpressionExperiment ee)	Obtain a BatchEffectType describing the batch effect state of the given experiment.
BatchEffectDetails	getBatchEffectDetails(ExpressionExperiment ee)	Obtain the full batch effect details of a given experiment.
String	getBatchEffectStatistics(ExpressionExperiment ee)	Obtain a string describing the summary statistics of a batch effect is present in the given experiment.
List<BatchConfound>	getSignificantBatchConfounds(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset.
Map<ExpressionExperimentSubSet,List<BatchConfound>>	getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset subsets.
boolean	hasSignificantBatchConfound(ExpressionExperiment ee)	Check if a given experiment has a significant batch confound.

Method Detail

checkHasBatchInfo

boolean checkHasBatchInfo(ExpressionExperiment ee)

Check if the given experiment has batch information.

This does not imply that the batch information is usable or valid. Use checkHasUsableBatchInfo(ExpressionExperiment) for that purpose.

checkHasUsableBatchInfo

boolean checkHasUsableBatchInfo(ExpressionExperiment ee)

Check if the given experiment has usable batch information.

hasSignificantBatchConfound

boolean hasSignificantBatchConfound(ExpressionExperiment ee)

Check if a given experiment has a significant batch confound.

getSignificantBatchConfounds

List<BatchConfound> getSignificantBatchConfounds(ExpressionExperiment ee)

Obtain the significant batch confounds for a dataset.

getSignificantBatchConfoundsForSubsets

Map<ExpressionExperimentSubSet,List<BatchConfound>> getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)

Obtain the significant batch confounds for a dataset subsets.

getBatchConfoundAsHtmlString

@Nullable
String getBatchConfoundAsHtmlString(ExpressionExperiment ee)

Summarize the batch confounds for a given dataset or its subsets in an HTML string.

Returns:

a summary or null if there is no batch confound

getBatchEffectDetails

BatchEffectDetails getBatchEffectDetails(ExpressionExperiment ee)

Obtain the full batch effect details of a given experiment.

Parameters:

ee - experiment

Returns:

details for the principal component most associated with batches (even if it isn't "significant"). Note that we don't look at every component, just the first few.

getBatchEffect

BatchEffectType getBatchEffect(ExpressionExperiment ee)

Obtain a BatchEffectType describing the batch effect state of the given experiment.

Parameters:

ee - the experiment to get the batch effect for.

getBatchEffectStatistics

@Nullable
String getBatchEffectStatistics(ExpressionExperiment ee)

Obtain a string describing the summary statistics of a batch effect is present in the given experiment.

Returns:

summary statistics or null if there is no batch effect