Package ubic.gemma.core.analysis.preprocess

Interface TwoChannelMissingValues

All Known Implementing Classes:

TwoChannelMissingValuesImpl

public interface TwoChannelMissingValues

Field Summary

Fields

Modifier and Type	Field	Description
static double	DEFAULT_SIGNAL_TO_NOISE_THRESHOLD

Method Summary

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)

Field Detail

DEFAULT_SIGNAL_TO_NOISE_THRESHOLD

static final double DEFAULT_SIGNAL_TO_NOISE_THRESHOLD

See Also:

Constant Field Values

Method Detail

computeMissingValues

Collection<RawExpressionDataVector> computeMissingValues(ExpressionExperiment ee)

Parameters:

ee - The expression experiment to analyze. The quantitation types to use are selected automatically. If you want more control use other computeMissingValues methods.

Returns:

collection of raw expression data vectors

computeMissingValues

Collection<RawExpressionDataVector> computeMissingValues(ExpressionExperiment ee,
                                                         double signalToNoiseThreshold,
                                                         Collection<Double> extraMissingValueIndicators)

Parameters:

ee - The expression experiment to analyze. The quantitation types to use are selected automatically.

signalToNoiseThreshold - A value such as 1.5 or 2.0; only spots for which at least ONE of the channel signal is more than signalToNoiseThreshold*background (and the preferred data are not missing) will be considered present.

extraMissingValueIndicators - Values that should be considered missing. For example, some data sets use '0'. This can be null or empty and it will be ignored.

Returns:

DesignElementDataVectors corresponding to a new PRESENTCALL quantitation type for the experiment.