NAME
Microarray::Reporter - A Perl module for creating and manipulating microarray reporter objects
SYNOPSIS
my $oArray = microarray->new($barcode,$data_file);
$oArray->set_reporter_data;
my $oReporter = $oArray->get_reporter('RP11-354D4'); # returns a single reporter object
my $oReporter = array_reporter->new('reporter 1');
$oReporter->add_reporter_spot($oSpot);
$oReporter->do_spot_qc;
my $mean_log_ratio = $oReporter->mean_log_ratios;DESCRIPTION
Microarray::Reporter is an object-oriented Perl module for creating and manipulating microarray reporter objects. It serves as a container into which you place spot objects that are replicates of the same genetic reporter, and returns average information about those spots.
METHODS
- do_spot_qc
-
Performs QC on the spot level data. This uses a number of variables whose defaults are set by the Microarray module during initialisation of a Microarray object, and whose values can be changed using appropriate Microarray methods. The Microarray method should_reject_unique() causes the QC process to reject any reporter that contains only a single spot. It should be called on the microarray object before the set_reporter_data() method.
- reporter_id
-
Name of the reporter
- genetic_data
-
An object containing relevant genetic data.
- get_reporter_spots
-
Returns a list of spot objects attributed to a reporter
- get_reporter_replicates
-
Returns the number of spots attributed to a reporter
- spots_passed_qc
-
Returns the number of spots that passed QC criteria and are included in the reporter data
- mean_ch1 and mean_ch2
-
Mean signal of all spots representing a reporter
- mean_ratios and mean_log_ratios
-
Calculates the ratio (or log2 ratio) between the two signal channels for each replicate, and returns the mean of those values
- ratio_means and log_ratio_means
-
Calculates the mean of the replicate signals for each channel, and returns their ratio (or log2 ratio)
SEE ALSO
AUTHOR
Christopher Jones, Gynaecological Cancer Research Laboratories, Institute for Women's Health, University College London.
http://www.instituteforwomenshealth.ucl.ac.uk/AcademicResearch/Cancer/trl
c.jones@ucl.ac.uk
COPYRIGHT AND LICENSE
Copyright 2008 by Christopher Jones, University College London
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.