Class MaHybridSample

java.lang.Object
  |
  +--MaHybridSample

class MaHybridSample

extends java.lang.Object

The MaHybridSample class is the primary instance of hybridized sample array data. It includes all sample-specific image-dependent data such as xy coords, raw intensity(ies if both f1,f2 or f1/f2, etc. or Cy3, Cy5), background, QualCheck data, statistical descriptions of that data and calibration data. It also includes the data access methods used by all of the rest of MAExplorer. It initially invokes a MaHPquantTable instance to read the quantified data from the .quant data file. Note: The genomic ID info is kept in the list of Gene instances accessed through Maps.midStaticCL or Maps.gidStaticCL.

An instance of this class contains primary data describing a particular hybridized sample including: its name; full name; file name; channel(s) intensity, background, QualCheck flag, pseudoarray image and actual image spot coordinates, correlation coefficient, gidMap; Cy3/Cy5 channel swap state; statistics on total data and subsets of the data; scale factors for different normalizations; etc.

It includes many primary methods used throughout MAExplorer for accessing this data including:

List of methods
 lookupGeneFromXY() - lookup mid if find Point xy in sample HP pseudoarray image
 scaleIntensData() - scale raw intensity data as function of normalization mode
 cvRI2HistScale() - convert raw intensity to histogram scale data for the gid
 cvHist2RIscale() - convert histogram scale to raw intensity data for the gid
 calcIntensScaleExtrema() - calculate intensity scale factor extrema for current normalization mode
 getSpotDataStatic() - get a STATIC scaled spot data object for this gid
 getSpotData12Static() - get STATIC scaled spot data object for gid1, gid2
 getF1F2Data() - get list spot (F1,F2)'s intensity data for data filtered genes
 computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema
 getDataByGID() - get scaled intensity data specified by gid and data type
 getRawDataByGID() - get raw (possibly bkgrd corrected) data specified by gid and data type
 getRawIntens() - get spot (rawIntensity - rawBackground) data by gid and data type
 getRawBkgrd() - get raw background intensity specified by the gid
 calcIntensHist() - compute Filtered spot intensity histogram for this sample
 calcMeanCalDNA() - calculate mean and stdDev RAW intensity Calibration DNA
 calcMeanUseNormGeneSet() - calculate mean and stdDev RAW intensity
 swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for the sample
 clearHPglobalStats() - clear global array statistics before compute actual ranges
 recalcGlobalStats() - recalculate global array statistics for all or just Good Spots
 cvtRawQdataToMAEdata() - convert .quant data to MAE data using HP array data ms.(bkgrdQ,totQ)[]

 This work was produced by Peter Lemkin of the National Cancer
 Institute, an agency of the United States Government.  As a work of
 the United States Government there is no associated copyright.  It is
 offered as open source software under the Mozilla Public License
 (version 1.1) subject to the limitations noted in the accompanying
 LEGAL file. This notice must be included with the code. The MAExplorer 
 Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/07/07 21:40:41 $ $Revision: 1.18 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home, MaHPquantTable

Field Summary

(package private) float	BGAvgQ Average background for entire array
(package private) float	BGLowQ low background estimate for entire array
(package private) float	BGRmsQ RMS background for entire array
(package private) float	bkgrdQ raw background intensity, unscaled
(package private) float[]	bkgrdSpotQ list of raw background intensity data/spot, unscaled
(package private) static int	DATA_F1TOT type code: for f1 data
(package private) static int	DATA_F2TOT type code: for f2 data
(package private) static int	DATA_MEAN_F1F2TOT type code: for (f1+f2)/2 data
(package private) static int	DATA_RATIO_F1F2TOT type code: for f1/f2 data
(package private) boolean	dataAvailFromQuantFileFlag set if can get quant data data from .quant file
(package private) java.lang.String	databaseFileID (opt) DatabaseFileID used with some databases (eg.
(package private) boolean	dataFromStateFileFlag flag: set if can get data from .state file
(package private) float	deltaBin Filter hist: #bins/maxData-minData)
(package private) float	deltaHistBin total array: width of a logRatio histogram bin
(package private) float[]	detValueQ (opt) list of spot Detection Value within spot for all spots.
(package private) boolean	doRatioFlag flag: if maxFIELD==1 && useRatioDataFlag
(package private) java.awt.Point	downPoint [FUTURE] for dragging- could be used for defining rubber-band regions
private Filter	fc link to global Filter instance
(package private) boolean	flipRowsColsFlag flag: flip rows and columns
(package private) java.lang.String	fullStageText full Stage text name of hybridized sample used in menus, etc
private GeneClass	gct link to global GeneClass instance
(package private) int[]	gidMapQ map GridCoord id for [f][g][r][c] for each row of this sample's tData[].
(package private) float	gidMaxF1 gid for max intens values F1 in getF1F2list
(package private) float	gidMaxF2 gid for max intens values F2 in getF1F2list
(package private) float	gidMinF1 gid for min intens values F1 in getF1F2list
(package private) float	gidMinF2 gid for min intens values F2 in getF1F2list
(package private) boolean	hasActualXYcoordsFlag flag: set if have actual XY coords - not pseudoCoords
(package private) boolean	hasBkgrdPerSpotFlag flag: set if have bkgrd intens/spot
(package private) boolean	hasDetValueSpotDataFlag flag: if using spot data "CorrCoef" or "DetValue" field
(package private) boolean	hasQualChkFlag flag: if using "QualCheck" field
(package private) boolean	hasValidDataFlag flag: set if .quant array data is set up ok
(package private) boolean	hasXYimageCQflag flag: has xyImgCQ_X/Y[] data for Montage image
(package private) int[]	hist normalized intensity histogram [0:nBins]
(package private) java.lang.String	hpName basename hybridized sample DB file name without file extension
(package private) int	idxHP index in list of all samples (mae.hps.msList[]) for this HP sample
(package private) boolean	implicitFieldsFlag flag: set true if no "field" field
(package private) float	logDeltaBin total array: (mae.MAX_INTENSITY/logRange)
(package private) float	logMaxRatioRI total array: log maxRatioRI
(package private) float	logMaxRI total array: log of maxRI
(package private) float	logMean Filter hist: log of mean raw intensity
(package private) float	logMeanAbsDev Filter hist: log of mean absolute deviation raw intensity
(package private) float	logMeanAbsDevRI total array: Filter hist: log of mean absolute deviation raw intensity
(package private) float	logMeanRI total array: mean of log of rawIntensity
(package private) float	logMiddle total array: -logMinRatioRI for finding RI==1.0
(package private) float	logMinRatioRI total array: log minRatioRI
(package private) float	logMinRI total array: log of minRI
(package private) float	logRange total array: log ratio range [Rmin:Rmax]
(package private) float	logStdDev Filter hist: log of stdDev raw intensity
(package private) float	logStdDevRI total array: std dev of log of means
(package private) float	madHPri total array: rawIntens meanAbsDev, all genes in HP w/o bkgrd
(package private) MAExplorer	mae link to global MAExplorer instance
private Maps	map link to global Maps instance
(package private) float	maxDataF1 max intens values F1 in getF1F2list
(package private) float	maxDataF2 max intens values F2 in getF1F2list
(package private) float	maxDataS current norm: scaled max data
(package private) float	maxFV maximum and fractions of dynamic range
(package private) float	maxHistData total array: mode hist data value
(package private) float	maxIntens max intensity of histogram data
(package private) float	maxRatioRI total array: max(f1RI/f2RI) for all spots
(package private) float	maxRaw total array: if Ratio, maximum of range of F1 or F2 RawIntens
(package private) float	maxRawS current norm: scaled maxRaw data
(package private) float	maxRI total array: range of RI or ratio
(package private) float	maxRI1 total array: range of RawIntensity1
(package private) float	maxRI2 total array: range of RawIntensity2
(package private) float	mean Filter hist: mean raw intensity
(package private) float	meanAbsDev Filter hist: mean absolute deviation raw intensity
(package private) float	meanCalDNA mean 'calibration DNA' intensity
(package private) int	meanIdx Filter hist: index of mean raw intensity
(package private) float	meanIntens mean of histogram data
(package private) float	meanUseGeneSet mean 'User Filter Gene set' intensity
(package private) float	median Filter hist: median raw intensity
(package private) float	medianF1 median of F1 channel
(package private) float	medianF1Bkgd median background of F1 channel
(package private) float	medianF2 median of F2 channel if present
(package private) float	medianF2Bkgd median background of F2 channel if present
(package private) int	medianIdx Filter hist: index of median raw intensity
(package private) float	medianIntens median of histogram data
(package private) float	medianRI total array: median value of rawIntensity
(package private) java.lang.String	menuTitle string to use in Sample menu entry
(package private) float	minDataF1 min intens values F1 in getF1F2list
(package private) float	minDataF2 min intens values F2 in getF1F2list
(package private) float	minDataS current norm: scaled min data
(package private) float	minHistData total array: min hist data value
(package private) float	minIntens min intensity of histogram data
(package private) float	minRatioRI total array: min(f1RI/f2RI) for all spots
(package private) float	minRaw total array: if Ratio, minimum of range of F1 or F2 RawIntens
(package private) float	minRawS current norm: scaled minRaw data
(package private) float	minRI total array: range of RI or ratio
(package private) float	minRI1 total array: range of RawIntensity1
(package private) float	minRI2 total array: range of RawIntensity2
(package private) float	mnHPri total array: rawIntens mean, all genes in HP w/o bkgrd
(package private) float	mnHPri1 total array: rawIntens f1 mean, all genes in HP w/o bkgrd
(package private) float	mnHPri2 total array: rawIntens f2 mean, all genes in HP w/o bkgrd
(package private) float	mode Filter hist: mode raw intensity
(package private) int	modeIdx Filter hist: index of mode raw intensity
(package private) float	modeIntens mode of histogram data
(package private) float	modeRI total array: mode value of rawIntensity
(package private) int	nBins number of bins in histogram.
(package private) boolean	needLoginFlag flag: set if requires login for this HP for it's projectName
(package private) float	normFactor normalization factor for all intensity data so we can compare intensity between HP samples.
(package private) java.lang.String	oImageName (opt) original image filename
(package private) java.lang.String	prjName project this HP sample belongs to
(package private) float[]	qualChkQ (opt) list of spot specific quality check using Gene.XXX properties for all spots
(package private) float	ratioMedianBkgdScale may be set if Cy3/Cy5 median bkgrd scale correction
(package private) float	ratioMedianScale may be set if Cy3/Cy5 median scale correction.
(package private) java.lang.String	sampleID English name of the sample
(package private) float	scaleCalDNA scale factor for scaling by calDNA
(package private) float	scaleCalDNAto65K scale factor for scaling by calDNA but max for all HPs is 65K
(package private) float	scaleToMaxIV total array: maxFV/maxRIscale factor to compute max range
(package private) float	scaleUseGeneSet scale factor for 'User Filter Gene set'
(package private) float	scaleUseGeneSetTo65K scale factor for 'User Filter Gene Set' but max for all HPs is 65K
(package private) float	sdHPri total array: rawIntens StdDev, all genes in HP w/o bkgrd
(package private) float	sdHPri1 total array: rawIntens f1 StdDev, all genes in HP w/o bkgrd
(package private) float	sdHPri2 total array: rawIntens f2 StdDev, all genes in HP w/o bkgrd
private Statistics	stat link to global Statistics instance
(package private) float	stdDev Filter hist: std deviation raw intensity
(package private) float	stdDevCalDNA stddev 'calibration DNA' intensity
(package private) float	stdDevUseGeneSet stddev 'User Filter Gene Set' intensity
(package private) boolean	swapCy5Cy3DataFlag flag: swapped Cy3 (Field1) and Cy5 (Field 2) data
(package private) java.lang.String[]	textHP title for each HP grid
(package private) float[]	totQ list of raw intensity data/spot, unscaled
(package private) java.awt.Point	upPoint [FUTURE] for dragging- could be used for defining rubber-band regions
(package private) int[]	x_textQ position of X grid label for PseudoImage
(package private) int	xCmax total array: max X coord mapped to MAE coord
(package private) int	xCmin total array: min X coord mapped to MAE coord
(package private) java.awt.Point[]	xyCQ (X,Y) of data from original array (if present) mapped to MAExplorer coordinate system or generated for PseudoArray Image
(package private) int[]	xyImgCQ_X (opt) X original image X coords scaled by 2.0.
(package private) int[]	xyImgCQ_Y (opt) X original image X coords scaled by 2.0.
(package private) int[]	y_textQ position of Y grid label for PseudoImage
(package private) int	yCmax total array: max Y coord mapped to MAE coord
(package private) int	yCmin total array: min Y coord mapped to MAE coord

Constructor Summary

(package private)

MaHybridSample(MAExplorer mae, java.lang.String hybSampleName, java.lang.String sampleID, java.lang.String databaseFileID, java.lang.String oImageName, java.lang.String menuTitle, java.lang.String fullStageText, java.lang.String projectName, boolean needLoginFlag, boolean swapCy5Cy3DataFlag, int idxHybridSample) MaHybridSample() - constuctor for an instance of a Microarray hybridized sample data

Method Summary

(package private) boolean	calcIntensHist() calcIntensHist() - compute Filtered spot intensity histogram for this sample It gets the normalized data from SpotData.
(package private) boolean	calcIntensScaleExtrema() calcIntensScaleExtrema() - calculate intensity scale factor extrema for current normalization mode.
(package private) boolean	calcMeanCalDNA() calcMeanCalDNA() - calculate mean and stdDev RAW intensity Calibration DNA.
(package private) boolean	calcMeanUseNormGeneSet() calcMeanUseNormGeneSet() - calculate mean and stdDev RAW intensity.
(package private) void	clearHPglobalStats() clearHPglobalStats() - clear global array statistics before compute actual ranges
(package private) boolean	computeMinMaxF1F2Data(boolean useF1F2ratioFlag, boolean useAllGenesFlag) computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema.
(package private) float	cvHist2RIscale(float hData) cvHist2RIscale() - convert histogram scale to raw intensity data for the gid.
(package private) float	cvRI2HistScale(int gid) cvRI2HistScale() - convert raw intensity to histogram scale data for the gid.
(package private) boolean	cvtRawQdataToMAEdata(boolean screenGoodGenesFlag) cvtRawQdataToMAEdata() - convert .quant data to MAE data using HP array data ms.(bkgrdQ,totQ)[] Note: totQ is RawIntensity, or unscaled ratio RawIntensity1/RawIntensity2.
(package private) float	getDataByGID(int gid, boolean useF1F2ratioFlag, int type) getDataByGID() - get scaled intensity data specified by gid and data type.
(package private) int	getF1F2Data(float[] xList, float[] yList, int[] propList, GeneList ml, boolean setPropsFlag, boolean useF1F2ratioFlag, boolean filterByMLflag) getF1F2Data() - get list spot (F1,F2)'s intensity data for data filtered genes and return it in the xList[1:n] is the field 1 data, yList[0:n-1] is field 2 data and the property in propList[0:n-1].
(package private) float	getRawBkgrd(int gid) getRawBkgrd() - get raw background intensity specified by the gid.
(package private) float	getRawDataByGID(int gid, boolean useF1F2ratioFlag, int type) getRawDataByGID() - get raw data specified by gid and data type.
(package private) float	getRawIntens(int gid, boolean useF1F2ratioFlag) getRawIntens() - get spot (rawIntensity - rawBackground) data by gid and data type
(package private) SpotData	getSpotData12Static(int gid1, int gid2, boolean useF1F2ratioFlag) getSpotData12Static() - get STATIC scaled spot data object for gid1, gid2.
(package private) SpotData	getSpotDataStatic(int gid, boolean useF1F2ratioFlag) getSpotDataStatic() - get a STATIC scaled spot data object for this gid.
(package private) int	lookupGeneFromXY(java.awt.Point xy) lookupGeneFromXY() - lookup mid if find Point xy in sample HP pseudoarray image
(package private) boolean	readHPquantFile(int hpNbr) readHPquantFile() - read the hybridized sample Quant File.
(package private) boolean	recalcGlobalStats(boolean useGoodSpotsOnlyFlag) recalcGlobalStats() - recalculate global array statistics for all or just Good Spots.
(package private) float	scaleIntensData(float dataI) scaleIntensData() - scale raw intensity data as function of normalization mode.
(package private) float	scaleIntensData(float dataI, int gid) scaleIntensData() - scale raw intensity data as function of normalization mode.
private void	setupHybSampleData() setupHybSampleData() - setup for .quant file for this hybridized sample.
(package private) boolean	swapCy5Cy3AndReCalcStats() swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for this sample.
(package private) boolean	validateHybSample(java.lang.String projectName) validateHybSample() - validate if login is required for this sample for this project.

Methods inherited from class java.lang.Object

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

Field Detail

mae

MAExplorer mae

link to global MAExplorer instance

map

private Maps map

link to global Maps instance

fc

private Filter fc

link to global Filter instance

stat

private Statistics stat

link to global Statistics instance

gct

private GeneClass gct

link to global GeneClass instance

DATA_MEAN_F1F2TOT

static final int DATA_MEAN_F1F2TOT

type code: for (f1+f2)/2 data

DATA_RATIO_F1F2TOT

static final int DATA_RATIO_F1F2TOT

type code: for f1/f2 data

DATA_F1TOT

static final int DATA_F1TOT

type code: for f1 data

DATA_F2TOT

static final int DATA_F2TOT

type code: for f2 data

menuTitle

java.lang.String menuTitle

string to use in Sample menu entry

prjName

java.lang.String prjName

project this HP sample belongs to

fullStageText

java.lang.String fullStageText

full Stage text name of hybridized sample used in menus, etc

oImageName

java.lang.String oImageName

(opt) original image filename

sampleID

java.lang.String sampleID

English name of the sample

databaseFileID

java.lang.String databaseFileID

(opt) DatabaseFileID used with some databases (eg. mAdb)

hpName

java.lang.String hpName

basename hybridized sample DB file name without file extension

idxHP

int idxHP

index in list of all samples (mae.hps.msList[]) for this HP sample

minDataF1

float minDataF1

min intens values F1 in getF1F2list

minDataF2

float minDataF2

min intens values F2 in getF1F2list

maxDataF1

float maxDataF1

max intens values F1 in getF1F2list

maxDataF2

float maxDataF2

max intens values F2 in getF1F2list

gidMinF1

float gidMinF1

gid for min intens values F1 in getF1F2list

gidMinF2

float gidMinF2

gid for min intens values F2 in getF1F2list

gidMaxF1

float gidMaxF1

gid for max intens values F1 in getF1F2list

gidMaxF2

float gidMaxF2

gid for max intens values F2 in getF1F2list

meanIdx

int meanIdx

Filter hist: index of mean raw intensity

modeIdx

int modeIdx

Filter hist: index of mode raw intensity

medianIdx

int medianIdx

Filter hist: index of median raw intensity

maxFV

float maxFV

maximum and fractions of dynamic range

deltaBin

float deltaBin

Filter hist: #bins/maxData-minData)

mean

float mean

Filter hist: mean raw intensity

mode

float mode

Filter hist: mode raw intensity

median

float median

Filter hist: median raw intensity

stdDev

float stdDev

Filter hist: std deviation raw intensity

meanAbsDev

float meanAbsDev

Filter hist: mean absolute deviation raw intensity

logMean

float logMean

Filter hist: log of mean raw intensity

logStdDev

float logStdDev

Filter hist: log of stdDev raw intensity

logMeanAbsDev

float logMeanAbsDev

Filter hist: log of mean absolute deviation raw intensity

ratioMedianScale

float ratioMedianScale

may be set if Cy3/Cy5 median scale correction. It is estimated (medianF2/medianF1).

ratioMedianBkgdScale

float ratioMedianBkgdScale

may be set if Cy3/Cy5 median bkgrd scale correction

stdDevUseGeneSet

float stdDevUseGeneSet

stddev 'User Filter Gene Set' intensity

meanUseGeneSet

float meanUseGeneSet

mean 'User Filter Gene set' intensity

scaleUseGeneSet

float scaleUseGeneSet

scale factor for 'User Filter Gene set'

scaleUseGeneSetTo65K

float scaleUseGeneSetTo65K

scale factor for 'User Filter Gene Set' but max for all HPs is 65K

stdDevCalDNA

float stdDevCalDNA

stddev 'calibration DNA' intensity

meanCalDNA

float meanCalDNA

mean 'calibration DNA' intensity

scaleCalDNA

float scaleCalDNA

scale factor for scaling by calDNA

scaleCalDNAto65K

float scaleCalDNAto65K

scale factor for scaling by calDNA but max for all HPs is 65K

medianF1

float medianF1

median of F1 channel

medianF2

float medianF2

median of F2 channel if present

medianF1Bkgd

float medianF1Bkgd

median background of F1 channel

medianF2Bkgd

float medianF2Bkgd

median background of F2 channel if present

maxDataS

float maxDataS

current norm: scaled max data

minDataS

float minDataS

current norm: scaled min data

maxRawS

float maxRawS

current norm: scaled maxRaw data

minRawS

float minRawS

current norm: scaled minRaw data

downPoint

java.awt.Point downPoint

[FUTURE] for dragging- could be used for defining rubber-band regions

upPoint

java.awt.Point upPoint

[FUTURE] for dragging- could be used for defining rubber-band regions

textHP

java.lang.String[] textHP

title for each HP grid

x_textQ

int[] x_textQ

position of X grid label for PseudoImage

y_textQ

int[] y_textQ

position of Y grid label for PseudoImage

doRatioFlag

boolean doRatioFlag

flag: if maxFIELD==1 && useRatioDataFlag

swapCy5Cy3DataFlag

boolean swapCy5Cy3DataFlag

flag: swapped Cy3 (Field1) and Cy5 (Field 2) data

needLoginFlag

boolean needLoginFlag

flag: set if requires login for this HP for it's projectName

hasXYimageCQflag

boolean hasXYimageCQflag

flag: has xyImgCQ_X/Y[] data for Montage image

dataFromStateFileFlag

boolean dataFromStateFileFlag

flag: set if can get data from .state file

dataAvailFromQuantFileFlag

boolean dataAvailFromQuantFileFlag

set if can get quant data data from .quant file

hist

int[] hist

normalized intensity histogram [0:nBins]

nBins

int nBins

number of bins in histogram. will be MAExplorer.MAX_INTENSITY

medianIntens

float medianIntens

median of histogram data

meanIntens

float meanIntens

mean of histogram data

modeIntens

float modeIntens

mode of histogram data

maxIntens

float maxIntens

max intensity of histogram data

minIntens

float minIntens

min intensity of histogram data

normFactor

float normFactor

normalization factor for all intensity data so we can compare intensity between HP samples.

BGLowQ

float BGLowQ

low background estimate for entire array

BGAvgQ

float BGAvgQ

Average background for entire array

BGRmsQ

float BGRmsQ

RMS background for entire array

bkgrdQ

float bkgrdQ

raw background intensity, unscaled

bkgrdSpotQ

float[] bkgrdSpotQ

list of raw background intensity data/spot, unscaled

totQ

float[] totQ

list of raw intensity data/spot, unscaled

detValueQ

float[] detValueQ

(opt) list of spot Detection Value within spot for all spots. e.g. Affymetrix "Detection p-value", etc.

qualChkQ

float[] qualChkQ

(opt) list of spot specific quality check using Gene.XXX properties for all spots

gidMapQ

int[] gidMapQ

map GridCoord id for [f][g][r][c] for each row of this sample's tData[].

xyCQ

java.awt.Point[] xyCQ

(X,Y) of data from original array (if present) mapped to MAExplorer coordinate system or generated for PseudoArray Image

xyImgCQ_X

int[] xyImgCQ_X

(opt) X original image X coords scaled by 2.0. The (X,Y) mapped of original image was mapped to scaled down image for use in generating montage images.

xyImgCQ_Y

int[] xyImgCQ_Y

(opt) X original image X coords scaled by 2.0. The (X,Y) mapped of original image was mapped to scaled down image for use in generating montage images.

hasActualXYcoordsFlag

boolean hasActualXYcoordsFlag

flag: set if have actual XY coords - not pseudoCoords

hasBkgrdPerSpotFlag

boolean hasBkgrdPerSpotFlag

flag: set if have bkgrd intens/spot

hasQualChkFlag

boolean hasQualChkFlag

flag: if using "QualCheck" field

hasDetValueSpotDataFlag

boolean hasDetValueSpotDataFlag

flag: if using spot data "CorrCoef" or "DetValue" field

implicitFieldsFlag

boolean implicitFieldsFlag

flag: set true if no "field" field

flipRowsColsFlag

boolean flipRowsColsFlag

flag: flip rows and columns

hasValidDataFlag

boolean hasValidDataFlag

flag: set if .quant array data is set up ok

minHistData

float minHistData

total array: min hist data value

maxHistData

float maxHistData

total array: mode hist data value

mnHPri

float mnHPri

total array: rawIntens mean, all genes in HP w/o bkgrd

sdHPri

float sdHPri

total array: rawIntens StdDev, all genes in HP w/o bkgrd

madHPri

float madHPri

total array: rawIntens meanAbsDev, all genes in HP w/o bkgrd

mnHPri1

float mnHPri1

total array: rawIntens f1 mean, all genes in HP w/o bkgrd

sdHPri1

float sdHPri1

total array: rawIntens f1 StdDev, all genes in HP w/o bkgrd

mnHPri2

float mnHPri2

total array: rawIntens f2 mean, all genes in HP w/o bkgrd

sdHPri2

float sdHPri2

total array: rawIntens f2 StdDev, all genes in HP w/o bkgrd

scaleToMaxIV

float scaleToMaxIV

total array: maxFV/maxRIscale factor to compute max range

logMeanRI

float logMeanRI

total array: mean of log of rawIntensity

logStdDevRI

float logStdDevRI

total array: std dev of log of means

logMeanAbsDevRI

float logMeanAbsDevRI

total array: Filter hist: log of mean absolute deviation raw intensity

logMaxRI

float logMaxRI

total array: log of maxRI

logMinRI

float logMinRI

total array: log of minRI

medianRI

float medianRI

total array: median value of rawIntensity

modeRI

float modeRI

total array: mode value of rawIntensity

minRI

float minRI

total array: range of RI or ratio

maxRI

float maxRI

total array: range of RI or ratio

minRI1

float minRI1

total array: range of RawIntensity1

maxRI1

float maxRI1

total array: range of RawIntensity1

minRI2

float minRI2

total array: range of RawIntensity2

maxRI2

float maxRI2

total array: range of RawIntensity2

minRaw

float minRaw

total array: if Ratio, minimum of range of F1 or F2 RawIntens

maxRaw

float maxRaw

total array: if Ratio, maximum of range of F1 or F2 RawIntens

deltaHistBin

float deltaHistBin

total array: width of a logRatio histogram bin

maxRatioRI

float maxRatioRI

total array: max(f1RI/f2RI) for all spots

minRatioRI

float minRatioRI

total array: min(f1RI/f2RI) for all spots

logMaxRatioRI

float logMaxRatioRI

total array: log maxRatioRI

logMinRatioRI

float logMinRatioRI

total array: log minRatioRI

logRange

float logRange

total array: log ratio range [Rmin:Rmax]

logDeltaBin

float logDeltaBin

total array: (mae.MAX_INTENSITY/logRange)

logMiddle

float logMiddle

total array: -logMinRatioRI for finding RI==1.0

xCmax

int xCmax

total array: max X coord mapped to MAE coord

yCmax

int yCmax

total array: max Y coord mapped to MAE coord

xCmin

int xCmin

total array: min X coord mapped to MAE coord

yCmin

int yCmin

total array: min Y coord mapped to MAE coord

Constructor Detail

MaHybridSample

MaHybridSample(MAExplorer mae,
               java.lang.String hybSampleName,
               java.lang.String sampleID,
               java.lang.String databaseFileID,
               java.lang.String oImageName,
               java.lang.String menuTitle,
               java.lang.String fullStageText,
               java.lang.String projectName,
               boolean needLoginFlag,
               boolean swapCy5Cy3DataFlag,
               int idxHybridSample)

MaHybridSample() - constuctor for an instance of a Microarray hybridized sample data

Parameters:

mae - is instance of MAExplorer

hybSampleName - is the sample name

sampleID - is the free text form of the sample name

databaseFileID - is the (opt) database file ID

oImageName - is the image name

menuTitle - is the string used in Sample menu entry

fullStageText - is the full Stage text name

projectName - is the project this HP sample belongs

needLoginFlag - indicates that it requires login for projectName

swapCy5Cy3DataFlag - indicates that swap (Cy3,Cy5) data

idxHybridSample - is the index in hps.msList[] entry for this sample

See Also:

FileIO.logMsgln(java.lang.String), Util.showMsg(java.lang.String), setupHybSampleData(), validateHybSample(java.lang.String)

Method Detail

setupHybSampleData

private void setupHybSampleData()

setupHybSampleData() - setup for .quant file for this hybridized sample. This includes: reading .quant file, and setup grid mappings, default normalization constants.

See Also:

GridCoords.createIndexToGridCoordMap(), calcIntensScaleExtrema(), readHPquantFile(int)

validateHybSample

boolean validateHybSample(java.lang.String projectName)

validateHybSample() - validate if login is required for this sample for this project. Test if need to get user login to proceed. Check needLoginFlag which was set from HP entry in the Samples table if Login is set to true.

 If the user had already logged in and the project is the
    mae.validProjects[0:mae.nValidProjects-1] list, then don't
 check since already logged in.
 Otherwise, get the (uN,uPW) from popup dialog and then check
 with the server to see if the (uN,uPW,uPrj) is in the password file.

 If the login is OK, then it has the side effect of setting
   mae.curProjName= projectName;
   mae.isLoggedInFlag= true;
   this.needLoginFlag= false;
 Also push projectName into the list of projects.
   mae.validProjects[mae.nValidProjects++]

Parameters:

projectName - project name for this database

Returns:

true if login is OK.

See Also:

UserState.validateUserProject(java.lang.String, java.lang.String, java.lang.String)

readHPquantFile

boolean readHPquantFile(int hpNbr)

readHPquantFile() - read the hybridized sample Quant File. Note the .quant data files are in the /Quant subdirectory! [TODO] fixup so can use with mAdb CGI server.

Parameters:

hpNbr - is the sample number in the msList[] list of samples..

Returns:

false if failed.

See Also:

FileIO.logMsgln(java.lang.String), MaHPquantTable, MathMAE.logZero(double)

lookupGeneFromXY

int lookupGeneFromXY(java.awt.Point xy)

lookupGeneFromXY() - lookup mid if find Point xy in sample HP pseudoarray image

Parameters:

xy - is the xy coordinate near the spot.

Returns:

MID if found else -1.

scaleIntensData

float scaleIntensData(float dataI)

scaleIntensData() - scale raw intensity data as function of normalization mode. This is called on a per-spot basis. This calls the extended for with (mid,gid,sampleNbr)=(0,0,0).

Parameters:

dataI - is the raw intensity of a spot

Returns:

the scaled intensity

See Also:

MaeJavaAPI.getActiveNormalization(), MaeJavaAPI.getNormalizationState()

scaleIntensData

float scaleIntensData(float dataI,
                      int gid)

scaleIntensData() - scale raw intensity data as function of normalization mode. This method uses the gid and sample number (idxHP) in case it is needed. This is called on a per-spot basis.

Parameters:

dataI - is the raw intensity of a spot

gid - is GID of the spot

Returns:

the scaled intensity

See Also:

MaeJavaAPI.getActiveNormalization(), MaeJavaAPI.getNormalizationState()

cvRI2HistScale

float cvRI2HistScale(int gid)

cvRI2HistScale() - convert raw intensity to histogram scale data for the gid. The hist scale is [0:mae.MAX_INTENSITY-1].

 Get the raw intensity data for spot gid and scale to
  a) log(f1/f2) if ratio mode
  b) raw intensity for spot ms.scaleToMaxIV if > 65K
  c) else raw intensity for spot.

Parameters:

gid - is Grid Index ID

Returns:

histogram scaled data.

See Also:

MathMAE.logZero(double)

cvHist2RIscale

float cvHist2RIscale(float hData)

cvHist2RIscale() - convert histogram scale to raw intensity data for the gid. The hist scale is [0:mae.MAX_INTENSITY-1].

 Get raw intensity data inverse histogram data for
  a) log(f1/f2) if ratio mode
  b) raw intensity for spot ms.scaleToMaxIV if > 65K
  c) else raw intensity for spot.

Parameters:

hData - is the histogram value to be scaled

Returns:

histogram scaled data.

calcIntensScaleExtrema

boolean calcIntensScaleExtrema()

calcIntensScaleExtrema() - calculate intensity scale factor extrema for current normalization mode.

Returns:

true if successful.

See Also:

MaeJavaAPI.getActiveNormalization(), MaeJavaAPI.getNormalizationState()

getSpotDataStatic

SpotData getSpotDataStatic(int gid,
                           boolean useF1F2ratioFlag)

getSpotDataStatic() - get a STATIC scaled spot data object for this gid.

Parameters:

gid - is the Grid Index (GID)

useF1F2ratioFlag - to compute F1/F2 ratio data

Returns:

data instance else null if there is no data or there is a problem.

See Also:

SpotData.setSpotData(MaHybridSample, int, int, int, float), getRawIntens(int, boolean), scaleIntensData(float)

getSpotData12Static

SpotData getSpotData12Static(int gid1,
                             int gid2,
                             boolean useF1F2ratioFlag)

getSpotData12Static() - get STATIC scaled spot data object for gid1, gid2.

Parameters:

gid1 - is the Grid Index (GID) F1

gid2 - is the Grid Index (GID) F2

useF1F2ratioFlag - to compute F1/F2 ratio data

Returns:

data else null if there is no data or there is a problem.

See Also:

SpotData.setSpotData1(MaHybridSample, java.awt.Point, int, float), SpotData.setSpotData2(MaHybridSample, java.awt.Point, int, float), getRawIntens(int, boolean), scaleIntensData(float)

getF1F2Data

int getF1F2Data(float[] xList,
                float[] yList,
                int[] propList,
                GeneList ml,
                boolean setPropsFlag,
                boolean useF1F2ratioFlag,
                boolean filterByMLflag)

getF1F2Data() - get list spot (F1,F2)'s intensity data for data filtered genes and return it in the xList[1:n] is the field 1 data, yList[0:n-1] is field 2 data and the property in propList[0:n-1]. Also add the gene list data for each entry.

Parameters:

xList[max - # genes to get] Return F1 values

yList[max - # genes to get] Return optional F2 values

propList[max - # genes to get] gene property values

ml - is the GeneList to save genes in if not null or filter by GeneList. To filter by all genes, set ml to set of all genes mae.gct.allGenesCL

setPropsFlag - set the propList[] data from workingCL as IS_FILTERED or IS_NOT_FILTERED

useF1F2ratioFlag - pass onto getSpotData12Static()

filterByMLflag - if true, then filter by ml GeneList.

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

See Also:

Gene.setGeneData(float), GeneBitSet.isItemInGeneBitSet(int), GeneList.clearNull(), GeneList.setGene(Gene, int), Filter.isMIDinWorkingCL(int), getSpotData12Static(int, int, boolean)

computeMinMaxF1F2Data

boolean computeMinMaxF1F2Data(boolean useF1F2ratioFlag,
                              boolean useAllGenesFlag)

computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema. The results are saved in (minDataF1, minDataF2, maxDataF1, maxDataF2).

Parameters:

useF1F2ratioFlag - to compute F1/F2 ratio data

useAllGenesFlag - to use all genes else use the workingCL gene list

Returns:

true if succeed

See Also:

Filter.isMIDinWorkingCL(int), getSpotData12Static(int, int, boolean)

getDataByGID

float getDataByGID(int gid,
                   boolean useF1F2ratioFlag,
                   int type)

getDataByGID() - get scaled intensity data specified by gid and data type. Note: this may get the F1 and F2 data, its mean or its ratio. If it is ratio, then the data is precomputed in totQ[].

Parameters:

gid - is the Grid Index GID for spot

useF1F2ratioFlag - to compute F1/F2 ratio data

type - is DATA_MEAN_F1F2TOT or DATA_RATIO_F1F2TOT, DATA_F1TOT, or DATA_F2TOT

Returns:

data

See Also:

getSpotDataStatic(int, boolean), getSpotData12Static(int, int, boolean)

getRawDataByGID

float getRawDataByGID(int gid,
                      boolean useF1F2ratioFlag,
                      int type)

getRawDataByGID() - get raw data specified by gid and data type. If background correction is enabled, then return background corrected raw intensity. Note: this may get the F1 and F2 data, its mean or its ratio.

Parameters:

gid - is the GeneID GID for the spot

useF1F2ratioFlag - if set get the F1/F2 ratio else F1 data

type - is access method: DATA_MEAN_F1F2TOT, DATA_RATIO_F1F2TOT, DATA_F1TOT, or DATA_F2TOT

Returns:

raw intensity value for this sample

See Also:

getRawIntens(int, boolean)

getRawIntens

final float getRawIntens(int gid,
                         boolean useF1F2ratioFlag)

getRawIntens() - get spot (rawIntensity - rawBackground) data by gid and data type

 If background subtraction is enabled then
   I1= (signal1 - bkgrdQ1)and I2= (signal2 - bkgrdQ2).
 else
   I1= signal1, and I2= signal2.
 If using ratio data, then return ratio (I1/I2) else I1.
 If using ratioMedianScaling, then also multiply ratio data
 by scaling factor (ratioMedianScale if not subtracting
 background and by ratioMedianBkgdScale if we are subtracting
 background).

Parameters:

gid - is the Grid index ID GID for the spot

useF1F2ratioFlag - then return ratio of F1/F2 else F1.

Returns:

raw intensity value for this sample. If no sample is defined, then return 0.0F.

See Also:

Maps

getRawBkgrd

final float getRawBkgrd(int gid)

getRawBkgrd() - get raw background intensity specified by the gid. If using ratio data, then return ratio, else intensity data.

Parameters:

gid - is the Grid index ID GID for the spot

Returns:

data

calcIntensHist

boolean calcIntensHist()

calcIntensHist() - compute Filtered spot intensity histogram for this sample It gets the normalized data from SpotData. The data is scaled to the (minRI,maxRI) range of the data. It also computes (meanIntens, modeIntens, maxIntens, and minIntens).

Returns:

true if succeed

See Also:

Filter.isMIDinWorkingCL(int), Statistics.calcHistStats(java.lang.String, int, float[], int), cvHist2RIscale(float), getDataByGID(int, boolean, int)

calcMeanCalDNA

boolean calcMeanCalDNA()

calcMeanCalDNA() - calculate mean and stdDev RAW intensity Calibration DNA. These are saved in this instance of (meanCalDNA, stdDevCalDNA) The number of calibration DNA genes are in GeneNames.calDNACL.length

Returns:

true if successful.

See Also:

Statistics.calcHistStats(java.lang.String, int, float[], int), cvHist2RIscale(float), getRawDataByGID(int, boolean, int)

calcMeanUseNormGeneSet

boolean calcMeanUseNormGeneSet()

calcMeanUseNormGeneSet() - calculate mean and stdDev RAW intensity. These are saved in this instance of (meanUseGeneSet, stdDevUseGeneSet) The number of normCL genes are in fc.normCL.length

Returns:

true if successful.

See Also:

Statistics.calcHistStats(java.lang.String, int, float[], int), cvHist2RIscale(float), getRawDataByGID(int, boolean, int)

swapCy5Cy3AndReCalcStats

boolean swapCy5Cy3AndReCalcStats()

swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for this sample. toggle swapCy5Cy3DataFlag.

Returns:

true if succeed.

clearHPglobalStats

void clearHPglobalStats()

clearHPglobalStats() - clear global array statistics before compute actual ranges

recalcGlobalStats

boolean recalcGlobalStats(boolean useGoodSpotsOnlyFlag)

recalcGlobalStats() - recalculate global array statistics for all or just Good Spots.

Parameters:

useGoodSpotsOnlyFlag - to only use good spots in computing statistics.

Returns:

true if successful.

See Also:

clearHPglobalStats(), cvtRawQdataToMAEdata(boolean)

cvtRawQdataToMAEdata

boolean cvtRawQdataToMAEdata(boolean screenGoodGenesFlag)

cvtRawQdataToMAEdata() - convert .quant data to MAE data using HP array data ms.(bkgrdQ,totQ)[] Note: totQ is RawIntensity, or unscaled ratio RawIntensity1/RawIntensity2.
Compute the statistics (ms.mnHPiq, ms.sdHPiq) etc. for all data points in HP for: f1, f2, f1/f2.
If doing ratio (f1/f2), map log(f1/f2) to [0:mae.MAX_INTENSITY] do statistics and then map back to (f1/f2) space.

Parameters:

screenGoodGenesFlag - to only use good spots in computing statistics.

Returns:

true if successful.

See Also:

MathMAE.logZero(double), Statistics.calcHistStats(java.lang.String, int, float[], int), cvHist2RIscale(float), cvRI2HistScale(int)