Package ubic.gemma.core.analysis.preprocess.batcheffects

Interface BatchInfoPopulationHelperService

All Known Implementing Classes:

BatchInfoPopulationHelperServiceImpl

public interface BatchInfoPopulationHelperService

Author:

paul

Method Summary

Modifier and Type	Method	Description
ExperimentalFactor	createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Method Details

createRnaSeqBatchFactor

ExperimentalFactor createRnaSeqBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial,String> headers)

For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Parameters:

ee - experiment

headers - map of biomaterial to a string. If there was no usable FASTQ header, we just use the GPL ID

Returns:

factor

createBatchFactor

ExperimentalFactor createBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial,Date> dates)