NAME

Microarray::Spot - A Perl module for creating and manipulating microarray spot objects

SYNOPSIS

        use Microarray;

        my $oArray = microarray->new($barcode,$data_file);
        my $oData_File = $oArray->data_file;    # the data_file object
        my $oSpot = $oData_File->get_spots(123);
        my $ch2_signal = $oSpot->channel2_signal;
        my $log2_ratio = $oSpot->log2_ratio;

DESCRIPTION

Microarray::Spot is an object-oriented Perl module for creating and manipulating microarray spot objects. Spot data is imported from a Microarray::File::Data object and retrieved by calling any of the methods described below.

METHODS

spot_index

As defined in the data file, and/or the order the spot appeared in the data file

feature_id and synonym_id

Usually the 'Name' and 'ID' fields of the data file, respectively

channel1_signal and channel2_signal

BlueFuse data file objects set this value to the Spot object. For other formats the Spot object returns the background-subtracted signals (mean signal-median background)

channel1_snr and channel2_snr

Signal to noise ratio. Can be set by the data file object, otherwise the Spot object returns the median signal/background SD

channel1_quality and channel2_quality

For the ScanArray format, this is the percentage of pixels with signal more than 2 standard deviations above background

channel1_sat and channel2_sat

The percentage of pixels with a saturated signal

spot_diameter

Units are usually in microns

spot_pixels

The number of pixels depends on the scan resolution. This is usually defined in the data file header information from a scan

flag_id

If there is a flag associated with the spot, returns that number

spot_status

Indicates whether the spot was rejected by QC criteria (0=failed, 1=passed)

SEE ALSO

Microarray, Microarray::Reporter, Microarray::File, Microarray::File::Data

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.