Package ubic.gemma.core.analysis.preprocess.batcheffects
package ubic.gemma.core.analysis.preprocess.batcheffects
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ClassDescriptionExtract the scan date from Affymetrix CEL files.Because agilent makes slides that work with any scanner, the formats are not that predictable.Represents a summary of a batch effect confound.Test if an experimental design is confounded with batches.provide some basic information about the properties and strength of a batch effect, if any.Indicate that batch information is missing.Parse information on batch from raw data files.Used to indicate a problem with the population of batch information for a given
ExpressionExperiment.Retrieve batch information from the data source, if possible, and populate it into experiments.Retrieve batch information from the data source, if possible, and populate it into experiments.Methods for correcting batch effects.Provides status of batch information for datasets.Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.Looks through text file looking for a date near the top of the file in a reasonable format.Generic interface for classes that extract scan dates from raw data files.Indicates that batches with only a single sample were found, which means we don't form batches at all.Used to indicate failure was due to the format being unusable, but the files are available.