Microarray::File::Data::BlueFuse - A Perl module for managing BlueFuse 'output' files
=head1 SYNOPSIS
use Microarray::File::Data::BlueFuse;
my $data_file = bluefuse_file->new("/file.csv");
=head1 DESCRIPTION
Microarray::File::Data::BlueFuse is an object-oriented Perl module for managing microarray files created by BlueGnome's (L<http://www.bluegnome.co.uk/>) 'BlueFuse' software. It inherits from L<Microarray::File|Microarray::File>, and maps data fields in a BlueFuse 'output' data file to those used by L<Microarray::File::Data|Microarray::File::Data>.
Returns the confidence estimate range for each confidence flag. Passing a flag as an argument returns C<($start,$end)> for that flag. Alternatively if a list is requested it will return each division, starting at 0 and ending at 1, else will return a hashref of keys A to E and the range as an arrayref C<[$start,$end]>.
=item B<slide_barcode>
Odd - BlueFuse does not return the barcode in the file header. So it has to guess it using the data_file method C<guess_barcode()>. Have asked the nice people at BlueGnome if they can fix this, and apparently they might, one day.
Returns the percentage of spots with each confidence flag. Passing a flag as an argument returns only the value for that flag. Alternatively if a list is requested it will return a list of values for flags A to E, else will return a hashref of keys A to E and their respective flag values.
Actually return the AMPCH1 and AMPCH2 columns - the spot signal. The C<ch_mean_f> methods are provided for compatibility with other modules which calculate signal and background separately, and in which the calculated signal is returned using the methods C<channel1_signal> and C<channel2_signal>. As a result, the methods C<ch1_median_b> and C<ch2_median_b> are also provided in this module, but will always return '0'. However, other values for signal and background (such as C<snr, median_f, sd_f, mean_b> and C<sd_b>) are not returned and will generate an error.
=item B<x_pos>, B<y_pos>
The PELROW and PELCOL columns - the spot coordinates, returning the top/left position of the spot.
=item B<channel1_quality>, B<channel2_quality>
The P ON CH1 and P ON CH2 columns - estimates of the baysian probability that a biological signal is present in each channel
The 2*(RADIUS), UNIFORMITY, CIRCULARITY, QUALITY and GRID OFFSET columns.
=back
=head1 FUTURE DEVELOPMENT
At some point I plan to make this compatible with all of the BlueFuse file formats. While it has currently only been tested with the 'output' format, it might work with the other files.