Package ubic.gemma.core.loader.expression.geo.model

Class GeoDataset

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:

  • Field Details

  • Constructor Details

    • GeoDataset

      public GeoDataset()

  • Method Details

    • 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.

    • getSubsets

      public Collection<GeoSubset> getSubsets()
      Returns:
      Returns the subsets.

    • 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.