trans.qc
Class CelFileQualityControl

java.lang.Object
  trans.qc.CelFileQualityControl

public class CelFileQualityControl

extends java.lang.Object

Provides automated qc checking for cel files, flags those of poor quality based on a variety of statistics. For every cel file, the median intensity is calculated, then a median determined for all the cel files' medians, then a scaler is calculated for each cel file required to get it to the overall median. This is the cel file specific median scalar and indicates the degree of brighness relative to the other chips. After this calculation the intensities on all the chips are median scaled to the targetMedian defined in the application, ie 100. Lastly, all the stats are calculated on these scaled values. For the dim bright no synth calculations, these are made using the particular chip intensities, not any global values.

Author:

David Nix

Constructor Summary

CelFileQualityControl()

Method Summary

void	calculateMedianStatFlagValues() Calculates the median value for each stat flag
void	checkForFlippedControls() Runs through groups of cel files, calculates the median no Synth, Dim, and Bright intensities, checks to see if they are inverted, for some reason they sometimes are! Note these medians are calculated on the raw, pre scaled chip intensities.
void	checkSingleCelFileStats() Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.
void	cluster(int[][] pmCoordinates) Clusters cel files based on pm intensities by group.
void	clusterCelFiles(int[][] pmCoordinates) Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.
void	createCelFileStatsArray() Creates a cel file stats array, then saves and nulls the float arrays.
java.io.File[]	fetchCelFileStatsFiles()
java.lang.String	fetchQCParams()
void	instantiateStatFlags() Makes the Stat Flags, add new stats here.
static void	main(java.lang.String[] args)
void	makeCharts() Writes charts to the save directory and if so indicated displays them.
void	printCelFileStats() Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.
static void	printDocs()
void	printStatFlags() Prints name, median min max for each stat flag
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
java.lang.StringBuffer	statSingleCelFile(CelFileStats cs) Checks a CelStats object for deviations from the min max settings.
void	testCelFiles() Main app controler.
void	writePNGs(boolean restrictToOutlier) Writes PNG files for CelFileStats.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CelFileQualityControl

public CelFileQualityControl()

Method Detail

testCelFiles

public void testCelFiles()

Main app controler.

cluster

public void cluster(int[][] pmCoordinates)

Clusters cel files based on pm intensities by group.

makeCharts

public void makeCharts()

Writes charts to the save directory and if so indicated displays them.

checkForFlippedControls

public void checkForFlippedControls()

Runs through groups of cel files, calculates the median no Synth, Dim, and Bright intensities, checks to see if they are inverted, for some reason they sometimes are! Note these medians are calculated on the raw, pre scaled chip intensities.

printCelFileStats

public void printCelFileStats()

Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.

clusterCelFiles

public void clusterCelFiles(int[][] pmCoordinates)

Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.

checkSingleCelFileStats

public void checkSingleCelFileStats()

Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.

fetchCelFileStatsFiles

public java.io.File[] fetchCelFileStatsFiles()

writePNGs

public void writePNGs(boolean restrictToOutlier)

Writes PNG files for CelFileStats.

printStatFlags

public void printStatFlags()

Prints name, median min max for each stat flag

calculateMedianStatFlagValues

public void calculateMedianStatFlagValues()

Calculates the median value for each stat flag

instantiateStatFlags

public void instantiateStatFlags()

Makes the Stat Flags, add new stats here. Set

createCelFileStatsArray

public void createCelFileStatsArray()

Creates a cel file stats array, then saves and nulls the float arrays.

statSingleCelFile

public java.lang.StringBuffer statSingleCelFile(CelFileStats cs)

Checks a CelStats object for deviations from the min max settings. appends nothing if no errors.

main

public static void main(java.lang.String[] args)

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

fetchQCParams

public java.lang.String fetchQCParams()

printDocs

public static void printDocs()