ExpressionExperimentPlatformSwitchService (Gemma 1.31.6-SNAPSHOT API)

java.lang.Object
- ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
- - ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService

```
@Service
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 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 Description

ExpressionExperimentPlatformSwitchService()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign)`	If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform
`ArrayDesign`	`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
```
@Transactional
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
```
@Transactional
public ArrayDesign switchExperimentToMergedPlatform(ExpressionExperiment expExp)
```
    Automatically identify an appropriate merged platform
    
    Parameters:
    
    expExp - the experiment to switch to a merged platform
    
    Returns:
    
    the selected merged platform the experiment was switched to