ubic.gemma.core.loader.expression

Class ExpressionExperimentPlatformSwitchService

java.lang.Object

ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService

ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService

@Component
public class ExpressionExperimentPlatformSwitchService
extends ExpressionExperimentVectorManipulatingService

Switch an expression experiment from one array design to another. This is valuable when the EE uses more than on AD, and a merged AD exists. The following steps are needed:

• Delete old analyses of this experiment and processeddata vectors
• For each array design, for each probe, identify the matching probe on the merged AD. Have to deal with situation
• where more than one occurrence of each sequence is found.
• all DEDVs must be switched to use the new AD's design elements
• all bioassays must be switched to the new AD.
• update the EE description
• commit changes.
• Computed processed data vectors

This also handles the case of multisamples-per-platform - NOT the case of one-sample-per-platform but multiple platforms; for that you have to run VectorMerging. For more nutty situations this will probably create a mess.

Author:

pavlidis

See Also:

VectorMergingService

Field Summary

Fields

Modifier and Type	Field and Description
static BioSequence	NULL_BIOSEQUENCE Used to identify design elements that have no sequence associated with them.

Fields inherited from class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService

converter, processedExpressionDataVectorService, rawExpressionDataVectorService

Constructor Summary

Constructors

Constructor and Description
ExpressionExperimentPlatformSwitchService()

Method Summary

Modifier and Type	Method and Description
void	switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign) If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
void	switchExperimentToMergedPlatform(ExpressionExperiment expExp) Automatically identify an appropriate merged platform

Methods inherited from class ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService

convertFromBytes

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NULL_BIOSEQUENCE

public static final BioSequence NULL_BIOSEQUENCE

Used to identify design elements that have no sequence associated with them.

Constructor Detail

ExpressionExperimentPlatformSwitchService

public ExpressionExperimentPlatformSwitchService()

Method Detail

switchExperimentToArrayDesign

public void switchExperimentToArrayDesign(ExpressionExperiment ee,
                                          ArrayDesign arrayDesign)

If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform

Parameters:

ee - ee

arrayDesign - The array design to switch to. If some samples already use that array design, nothing will be changed for them.

switchExperimentToMergedPlatform

public void switchExperimentToMergedPlatform(ExpressionExperiment expExp)

Automatically identify an appropriate merged platform

Parameters:

expExp - ee