Christopher Jones > Microarray-0.45c > Microarray::Reporter

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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 ^

Microarray, Microarray::Spot

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.

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