ubic.gemma.core.analysis.expression.diff

Class DifferentialExpressionAnalysisUtil

java.lang.Object

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil

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

Constructor Summary

Constructors

Constructor and Description
DifferentialExpressionAnalysisUtil()

Method Summary

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DifferentialExpressionAnalysisUtil

public DifferentialExpressionAnalysisUtil()

Method Detail

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

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. factor

expressionExperiment - the experiment

Returns:

true if it's okay, false otherwise.

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