Microarray::Spot - A Perl module for creating and manipulating microarray spot objects
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;
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.
As defined in the data file, and/or the order the spot appeared in the data file
Usually the 'Name' and 'ID' fields of the data file, respectively
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)
Signal to noise ratio. Can be set by the data file object, otherwise the Spot object returns the median signal/background SD
For the ScanArray format, this is the percentage of pixels with signal more than 2 standard deviations above background
The percentage of pixels with a saturated signal
Units are usually in microns
The number of pixels depends on the scan resolution. This is usually defined in the data file header information from a scan
If there is a flag associated with the spot, returns that number
Indicates whether the spot was rejected by QC criteria (0=failed, 1=passed)
Christopher Jones, Gynaecological Cancer Research Laboratories, Institute for Women's Health, University College London.
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.