Author image Christopher Jones

Changes for version 0.45

  • Updated Microarray, Microarray::File::Data and Microarray::File::Data:: modules to use a more sensible 'Plug-In' architecture
  • Updated Microarray, Microarray::Image, Microarray::Image::QC_Plots and Microarray::Image::CGH_Plot to correct gdFont issues with latest release of GD
  • Reorganised QC of spot data
    • now performed by the Reporter object, not the Microarray object
    • added method to reject unique spots after QC
    • QC variables are now stored in $ENV
  • Fixed many bugs
  • Added new tests
    • image plotting in Microarray.pm, which also tests some of the Microarray::Image::QC_Plots code as well
    • image plotting in Microarray::Image::CGH_Plot.pm
    • image plotting tests need extra test files downloadable from our web site - see ReadMe
    • Microarray::Reporter
  • Resolved some errors in Perldoc left over from earlier changes to module namespace
  • Other Perldoc changes/updates

Modules

A Perl module for creating and manipulating DNA Microarray experiment objects
A Perl module for analysing microarray data
A Perl module for analysing CGH microarray data
Perl objects for handling microarray file formats
An object oriented Perl module describing a genomic clone location file
An object oriented Perl module describing microarray data files
A Perl module for managing Agilent microarray files
A Perl module for managing BlueFuse 'output' files
A Perl module for managing microarray Axon GenePix data files
A Perl module for managing 'Manor' clone and spot level output
A Perl module for managing Perkin Elmer 'Scanarray' microarray files
A Perl module for managing microarray GAL file objects
Perl objects for handling microarray image file formats
A Perl module for creating microarray data plots
A Perl module for creating CGH-microarray data plots
A Perl module for creating microarray QC/QA plots
A Perl module for creating and manipulating microarray reporter objects
A Perl module for creating and manipulating microarray spot objects

Provides

in lib/Microarray/File/Data/Agilent.pm
in lib/Microarray/Analysis.pm
in lib/Microarray/Reporter.pm
in lib/Microarray/Spot.pm
in lib/Microarray/File/Data/BlueFuse.pm
in lib/Microarray/File/Data/BlueFuse.pm
in lib/Microarray/Analysis/CGH.pm
in lib/Microarray/Image/CGH_Plot.pm
in lib/Microarray/Analysis/CGH.pm
in lib/Microarray/File/Clone_Locns.pm
in lib/Microarray/File/Data.pm
in lib/Microarray/File.pm
in lib/Microarray/File/GAL.pm
in lib/Microarray/File/Data/GenePix.pm
in lib/Microarray/File/Data/GenePix.pm
in lib/Microarray/Analysis/CGH.pm
in lib/Microarray/Image/CGH_Plot.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/File.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/File/Data/Manor_Output.pm
in lib/Microarray.pm
in lib/Microarray/File.pm
in lib/Microarray/File/Image.pm
in lib/Microarray/File.pm
in lib/Microarray/Image.pm
in lib/Microarray/File/Data/Quantarray.pm
in lib/Microarray/File/Data/Quantarray.pm
in lib/Microarray/Image/QC_Plots.pm
in lib/Microarray/File.pm