java.lang.Object
- ubic.gemma.core.loader.expression.geo.model.GeoData
- - ubic.gemma.core.loader.expression.geo.model.GeoDataset

All Implemented Interfaces:

Serializable
```
public class GeoDataset
extends GeoData
```
A GEO-curated dataset. In many cases this is associated with just one GeoSeries, but for studies that used more than one type of microarray (e.g., A and B chips in Affy sets), there will be two series.

Author:

pavlidis

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`GeoDataset.ExperimentType`
`static class`	`GeoDataset.PlatformType`
`static class`	`GeoDataset.SampleType`
`static class`	`GeoDataset.ValueType`

Field Summary

Fields
Modifier and Type Field Description

GeoDataset.ExperimentType experimentType
- Fields inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData
  contact, geoAccession

Constructor Summary

Constructors
Constructor Description

GeoDataset()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addSeries(GeoSeries newSeries)`
`void`	`addSubset(GeoSubset subset)`
`static GeoDataset.ExperimentType`	`convertStringToExperimentType(String string)`	gene expression array-based, gene expression SAGE-based, gene expression MPSS-based, gene expression RT-PCR-based, protein expression array-based, protein expression MS-based, array CGH, ChIP-chip, SNP Complete list of possibilities according to Nathaniel (6/2018) Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Non-coding RNA profiling by array Genome variation profiling by genome tiling array Genome variation profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing Genome variation profiling by SNP array SNP genotyping by SNP array Expression profiling by genome tiling array Genome variation profiling by array Expression profiling by RT-PCR Methylation profiling by high throughput sequencing Genome binding/occupancy profiling by genome tiling array Methylation profiling by genome tiling array Methylation profiling by array Genome binding/occupancy profiling by array Expression profiling by SAGE Protein profiling by protein array Genome binding/occupancy profiling by SNP array Non-coding RNA profiling by genome tiling array Third-party reanalysis Expression profiling by MPSS Expression profiling by SNP array Methylation profiling by SNP array Protein profiling by Mass Spec
`static GeoDataset.PlatformType`	`convertStringToPlatformType(String string)`
`static GeoDataset.SampleType`	`convertStringToSampleType(String string)`
`static GeoDataset.ValueType`	`convertStringToValueType(String string)`	count, log ratio, log2 ratio, log10 ratio, logE ratio, log e ratio, transformed count
`void`	`dissociateFromSeries(GeoSeries s)`	This is used when we break a series up into two, along organism lines.
`String`	`getCompleteness()`
`String`	`getDatasetType()`
`String`	`getDescription()`
`GeoDataset.ExperimentType`	`getExperimentType()`
`String`	`getFeatureCount()`
`int`	`getNumChannels()`
`int`	`getNumProbes()`
`int`	`getNumSamples()`
`String`	`getOrder()`
`String`	`getOrganism()`
`GeoPlatform`	`getPlatform()`
`GeoDataset.PlatformType`	`getPlatformType()`
`String`	`getPubmedId()`
`GeoDataset.SampleType`	`getSampleType()`
`Collection<GeoSeries>`	`getSeries()`
`Collection<GeoSubset>`	`getSubsets()`
`String`	`getUpdateDate()`
`GeoDataset.ValueType`	`getValueType()`
`void`	`setCompleteness(String completeness)`
`void`	`setDatasetType(String datasetType)`
`void`	`setDescription(String description)`
`void`	`setExperimentType(GeoDataset.ExperimentType experimentType)`
`void`	`setFeatureCount(String featureCount)`
`void`	`setNumChannels(int numChannels)`
`void`	`setNumProbes(int numProbes)`
`void`	`setNumSamples(int numSamples)`
`void`	`setOrder(String order)`
`void`	`setOrganism(String organism)`
`void`	`setPlatform(GeoPlatform platform)`
`void`	`setPlatformType(GeoDataset.PlatformType platformType)`
`void`	`setPubmedId(String pubmedId)`
`void`	`setSampleType(GeoDataset.SampleType sampleType)`
`void`	`setSeries(Collection<GeoSeries> series)`
`void`	`setSubsets(Collection<GeoSubset> subsets)`
`void`	`setUpdateDate(String updateDate)`
`void`	`setValueType(GeoDataset.ValueType valueType)`

Methods inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData
addColumnName, equals, getColumnDescriptions, getColumnNames, getContact, getGeoAccession, getTitle, hashCode, setGeoAccession, setTitle, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - experimentType
```
public GeoDataset.ExperimentType experimentType
```
- Constructor Detail
  - GeoDataset
```
public GeoDataset()
```
- Method Detail
  - convertStringToExperimentType
```
public static GeoDataset.ExperimentType convertStringToExperimentType(String string)
```
    gene expression array-based, gene expression SAGE-based, gene expression MPSS-based, gene expression RT-PCR-based, protein expression array-based, protein expression MS-based, array CGH, ChIP-chip, SNP Complete list of possibilities according to Nathaniel (6/2018) Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Non-coding RNA profiling by array Genome variation profiling by genome tiling array Genome variation profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing Genome variation profiling by SNP array SNP genotyping by SNP array Expression profiling by genome tiling array Genome variation profiling by array Expression profiling by RT-PCR Methylation profiling by high throughput sequencing Genome binding/occupancy profiling by genome tiling array Methylation profiling by genome tiling array Methylation profiling by array Genome binding/occupancy profiling by array Expression profiling by SAGE Protein profiling by protein array Genome binding/occupancy profiling by SNP array Non-coding RNA profiling by genome tiling array Third-party reanalysis Expression profiling by MPSS Expression profiling by SNP array Methylation profiling by SNP array Protein profiling by Mass Spec
    
    Parameters:
    
    string - experiment type string
    
    Returns:
    
    experiment type object
  - convertStringToPlatformType
```
public static GeoDataset.PlatformType convertStringToPlatformType(String string)
```
  - convertStringToSampleType
```
public static GeoDataset.SampleType convertStringToSampleType(String string)
```
  - convertStringToValueType
```
public static GeoDataset.ValueType convertStringToValueType(String string)
```
    count, log ratio, log2 ratio, log10 ratio, logE ratio, log e ratio, transformed count
    
    Parameters:
    
    string - value type string
    
    Returns:
    
    value type object
  - addSeries
```
public void addSeries(GeoSeries newSeries)
```
    Parameters:
    
    newSeries - geo series
  - addSubset
```
public void addSubset(GeoSubset subset)
```
  - dissociateFromSeries
```
public void dissociateFromSeries(GeoSeries s)
```
    This is used when we break a series up into two, along organism lines.
    
    Parameters:
    
    s - geo series
  - getCompleteness
```
public String getCompleteness()
```
    Returns:
    
    Returns the completeness.
  - setCompleteness
```
public void setCompleteness(String completeness)
```
    Parameters:
    
    completeness - The completeness to set.
  - getDatasetType
```
public String getDatasetType()
```
    Returns:
    
    Returns the datasetType.
  - setDatasetType
```
public void setDatasetType(String datasetType)
```
    Parameters:
    
    datasetType - The datasetType to set.
  - getDescription
```
public String getDescription()
```
    Returns:
    
    Returns the description.
  - setDescription
```
public void setDescription(String description)
```
    Parameters:
    
    description - The description to set.
  - getExperimentType
```
public GeoDataset.ExperimentType getExperimentType()
```
    Returns:
    
    Returns the experimentType.
  - setExperimentType
```
public void setExperimentType(GeoDataset.ExperimentType experimentType)
```
    Parameters:
    
    experimentType - The experimentType to set.
  - getFeatureCount
```
public String getFeatureCount()
```
    Returns:
    
    Returns the featureCount.
  - setFeatureCount
```
public void setFeatureCount(String featureCount)
```
    Parameters:
    
    featureCount - The featureCount to set.
  - getNumChannels
```
public int getNumChannels()
```
    Returns:
    
    Returns the numChannels.
  - setNumChannels
```
public void setNumChannels(int numChannels)
```
    Parameters:
    
    numChannels - The numChannels to set.
  - getNumSamples
```
public int getNumSamples()
```
    Returns:
    
    Returns the numSamples.
  - setNumSamples
```
public void setNumSamples(int numSamples)
```
    Parameters:
    
    numSamples - The numSamples to set.
  - getNumProbes
```
public int getNumProbes()
```
  - setNumProbes
```
public void setNumProbes(int numProbes)
```
  - getOrder
```
public String getOrder()
```
    Returns:
    
    Returns the order.
  - setOrder
```
public void setOrder(String order)
```
    Parameters:
    
    order - The order to set.
  - getOrganism
```
public String getOrganism()
```
    Returns:
    
    Returns the organism.
  - setOrganism
```
public void setOrganism(String organism)
```
    Parameters:
    
    organism - The organism to set.
  - getPlatform
```
public GeoPlatform getPlatform()
```
    Returns:
    
    Returns the platform.
  - setPlatform
```
public void setPlatform(GeoPlatform platform)
```
    Parameters:
    
    platform - The platform to set.
  - getPlatformType
```
public GeoDataset.PlatformType getPlatformType()
```
    Returns:
    
    Returns the probeType.
  - setPlatformType
```
public void setPlatformType(GeoDataset.PlatformType platformType)
```
  - getPubmedId
```
public String getPubmedId()
```
    Returns:
    
    Returns the pubmedId.
  - setPubmedId
```
public void setPubmedId(String pubmedId)
```
    Parameters:
    
    pubmedId - The pubmedId to set.
  - getSampleType
```
public GeoDataset.SampleType getSampleType()
```
    Returns:
    
    Returns the sampleType.
  - setSampleType
```
public void setSampleType(GeoDataset.SampleType sampleType)
```
    Parameters:
    
    sampleType - The sampleType to set.
  - getSeries
```
public Collection<GeoSeries> getSeries()
```
    Returns:
    
    Returns the series.
  - setSeries
```
public void setSeries(Collection<GeoSeries> series)
```
    Parameters:
    
    series - The series to set.
  - getSubsets
```
public Collection<GeoSubset> getSubsets()
```
    Returns:
    
    Returns the subsets.
  - setSubsets
```
public void setSubsets(Collection<GeoSubset> subsets)
```
    Parameters:
    
    subsets - The subsets to set.
  - getUpdateDate
```
public String getUpdateDate()
```
    Returns:
    
    Returns the updateDate.
  - setUpdateDate
```
public void setUpdateDate(String updateDate)
```
    Parameters:
    
    updateDate - The updateDate to set.
  - getValueType
```
public GeoDataset.ValueType getValueType()
```
    Returns:
    
    Returns the valueType.
  - setValueType
```
public void setValueType(GeoDataset.ValueType valueType)
```
    Parameters:
    
    valueType - The valueType to set.

Class GeoDataset

Nested Class Summary

Field Summary

Fields inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.core.loader.expression.geo.model.GeoData

Methods inherited from class java.lang.Object

Field Detail

experimentType

Constructor Detail

GeoDataset

Method Detail

convertStringToExperimentType

convertStringToPlatformType

convertStringToSampleType

convertStringToValueType

addSeries

addSubset

dissociateFromSeries

getCompleteness

setCompleteness

getDatasetType

setDatasetType

getDescription

setDescription

getExperimentType

setExperimentType

getFeatureCount

setFeatureCount

getNumChannels

setNumChannels

getNumSamples

setNumSamples

getNumProbes

setNumProbes

getOrder

setOrder

getOrganism

setOrganism

getPlatform

setPlatform

getPlatformType

setPlatformType

getPubmedId

setPubmedId

getSampleType

setSampleType

getSeries

setSeries

getSubsets

setSubsets

getUpdateDate

setUpdateDate

getValueType

setValueType