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

Class 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

    • 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

      • 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.

      • 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.

      • getPubmedId

        public String getPubmedId()
        Returns:
        Returns the pubmedId.

      • setPubmedId

        public void setPubmedId​(String pubmedId)
        Parameters:
        pubmedId - The pubmedId to set.

      • setSampleType

        public void setSampleType​(GeoDataset.SampleType sampleType)
        Parameters:
        sampleType - The sampleType to set.

      • getUpdateDate

        public String getUpdateDate()
        Returns:
        Returns the updateDate.

      • setUpdateDate

        public void setUpdateDate​(String updateDate)
        Parameters:
        updateDate - The updateDate to set.

      • setValueType

        public void setValueType​(GeoDataset.ValueType valueType)
        Parameters:
        valueType - The valueType to set.