Class DifferentialExpressionAnalysisUtil
- java.lang.Object
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- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
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public class DifferentialExpressionAnalysisUtil extends Object
A helper class for the differential expression analyzers. This class contains helper methods commonly needed when performing an analysis.- Author:
- keshav
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Constructor Summary
Constructors Constructor Description DifferentialExpressionAnalysisUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static boolean
blockComplete(BioAssaySet expressionExperiment, Collection<ExperimentalFactor> factors)
Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise.static boolean
checkValidForLm(BioAssaySet expressionExperiment, ExperimentalFactor experimentalFactor)
Check that the factorValues are measurements, or that there are at least two assays for at least one factor value.static List<BioMaterial>
getBioMaterialsForBioAssays(ExpressionDataMatrix<?> matrix)
Returns a List of all the different types of biomaterials across all bioassays in the experiment.
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Method Detail
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blockComplete
public static boolean blockComplete(BioAssaySet expressionExperiment, Collection<ExperimentalFactor> factors)
Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise. When determining completeness, a biomaterial's factor values are only considered if they are equivalent to one of the input experimental factors.- Parameters:
factors
- to consider completeness for.expressionExperiment
- the experiment- Returns:
- true if block complete
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checkValidForLm
public static boolean checkValidForLm(BioAssaySet expressionExperiment, ExperimentalFactor experimentalFactor)
Check that the factorValues are measurements, or that there are at least two assays for at least one factor value. Otherwise the model fit will be perfect and pvalues will not be returned.- Parameters:
experimentalFactor
- exp. factorexpressionExperiment
- the experiment- Returns:
- true if it's okay, false otherwise.
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getBioMaterialsForBioAssays
public static List<BioMaterial> getBioMaterialsForBioAssays(ExpressionDataMatrix<?> matrix)
Returns a List of all the different types of biomaterials across all bioassays in the experiment.- Parameters:
matrix
- matrix- Returns:
- list of biomaterials
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