MAEPlugin
Interface Normalization

All Known Implementing Classes:

NormalizationPlugin

public interface Normalization

Method Summary

float[]	calcIntensityScaleExtrema(float maxRI, float minRI, float maxRaw, float minRaw, int sampleNbr) calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample.
boolean	finishPipeline(int optArg) finishPipeline() - finish filter at end of normalization of all genes (if required).
java.lang.Object	getSample() getSample() - get the sample object
boolean	getState() getState() - get the state of the checkbox
void	recalcNormalizationExtrema() recalcNormalizationExtrema() - set the extreama for all samples for this plugin
boolean	resetPipeline(int optArg) resetPipeline() - reset filter at start of data Normalization.
float	scaleIntensityData(float rawData) scaleIntensityData() - scale raw intensity data as fct of normalization mode.
float	scaleIntensityData(float rawIntensity, float rawBkgrd, int mid, int gid, int sampleIdx) scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
float	scaleIntensityData(float rawData, int mid, int gid, int sampleNbr) scaleIntensityData() - scale raw intensity data as fct of normalization mode.
void	setSample(java.lang.Object o) setSample() - set the sample object
void	setState(boolean flag) setState() - set the state of the checkbox

Method Detail

calcIntensityScaleExtrema

public float[] calcIntensityScaleExtrema(float maxRI,
                                         float minRI,
                                         float maxRaw,
                                         float minRaw,
                                         int sampleNbr)

calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample. It is called to get extrema for use in scaling displays and other computations where the limits must be known.

Parameters:

maxRI - maximum raw ratio intensity

minRI - minimum raw ratio intensity

maxRaw - maximum raw intensity max(rawF1,rawF2)

minRaw - minimum raw intensity min(rawF1,rawF2)

sampleNbr - for the sample sample number in the range [1:maxSamples]

Returns:

an array with the following scaled data:

   element 0 = maxDataS
   element 1 = minDataS
   element 2 = maxRawS
   element 3 = minRawS

resetPipeline

public boolean resetPipeline(int optArg)

resetPipeline() - reset filter at start of data Normalization. We will test for ALL GENES (if required) using the midOK[] boolean created here to later determine if we actually perform the test. This sets up the state that may be used during the pipeline operation.

Parameters:

optArg - - optional argument

Returns:

true if succeed

finishPipeline

public boolean finishPipeline(int optArg)

finishPipeline() - finish filter at end of normalization of all genes (if required). This may be used to clean up the state after the pipeline operation.

Parameters:

optArg - - optional argument

Returns:

true if succeed

scaleIntensityData

public float scaleIntensityData(float rawData)

scaleIntensityData() - scale raw intensity data as fct of normalization mode. This method is called on a per-spot basis.

Parameters:

rawData - is unnormalized data of spot

Returns:

normalized spot data

scaleIntensityData

public float scaleIntensityData(float rawData,
                                int mid,
                                int gid,
                                int sampleNbr)

scaleIntensityData() - scale raw intensity data as fct of normalization mode. This method passes the (gid,sampleNbr) in case it is needed. This method is called on a per-spot basis.

Parameters:

rawData - is unnormalized data of spot

mid - is MID of the spot

gid - is GID of the spot

sampleNbr - for the sample array

Returns:

normalized spot data

scaleIntensityData

public float scaleIntensityData(float rawIntensity,
                                float rawBkgrd,
                                int mid,
                                int gid,
                                int sampleIdx)

scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis. If the normalization is inoperative, then just return 0.0. The mid must be >=0 since -1 indicates an illegal gene. The midOK[mid] must be true, else it indicates an illegal gene. [NOTE] The plugin writer should try to avoid doing special analyses here that need to be computed DURING the processing and instead do the computations during the resetPipeline() operation if possible. That may be able to optimized and the data cached to avoid constant recomputation.

Parameters:

rawIntensity - is intensity value to be normalized

rawBkgrd - is background intensity to be used in normalization if the use Background flag is set.

mid - is the Master Gene ID to test if not -1 and the gene exists

gid - is the spot Geometry Gene Index to test if not -1 and the spot exists

sampleIdx - is the HybridSample index number for single sample HP-X or HP-Y. For Cy3 vs Cy5 mode, it is 0 for Cy3 (F1), and 1 for Cy5 (F2). For HP-X 'set' vs HP-Y 'set' mode, it is 0 for HP-X 'set', and 1 for HP-Y 'set'

Returns:

scaled data if normalization is active, else 0.0F

getState

public boolean getState()

getState() - get the state of the checkbox

setState

public void setState(boolean flag)

setState() - set the state of the checkbox

recalcNormalizationExtrema

public void recalcNormalizationExtrema()

recalcNormalizationExtrema() - set the extreama for all samples for this plugin

setSample

public void setSample(java.lang.Object o)

setSample() - set the sample object

getSample

public java.lang.Object getSample()

getSample() - get the sample object