NAME

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

SYNOPSIS

use Microarray;

my $spot = array_spot->new('spot 1');
$spot->channel1_signal(32423);
$spot->channel2_signal(29478);

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

The background-subtracted signals (mean signal-median background)

channel1_snr and channel2_snr

Signal to noise ratio. For the ScanArray format, this is median signal/background SD. For most other formats this is signal/background

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::Feature, Microarray::File, Microarray::File::Data

AUTHOR

Christopher Jones, Translational Research Laboratories, Institute for Women's Health, University College London.

http://www.instituteforwomenshealth.ucl.ac.uk/trl

c.jones@ucl.ac.uk

COPYRIGHT AND LICENSE

Copyright 2006 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.