NAME

Microarray::File::Data::BlueFuse - A Perl module for managing BlueFuse 'output' files

SYNOPSIS

        use Microarray::File::Data::BlueFuse;
        my $data_file = bluefuse_file->new("/file.csv");

DESCRIPTION

Microarray::File::Data::BlueFuse is an object-oriented Perl module for managing microarray files created by BlueGnome's (http://www.bluegnome.co.uk/) 'BlueFuse' software. It inherits from Microarray::File, and maps data fields in a BlueFuse 'output' data file to those used by Microarray::File::Data.

METHODS

General Header Information

analysis_software, build, experiment, frame_ch1, frame_ch2, gal_file, clone_file, clone_text, channel1_image_file, channel2_image_file

These methods all return the relevant header information as a scalar.

confidence_flag_range, confidence_flag_range($flag)

Returns the confidence estimate range for each confidence flag. Passing a flag as an argument returns ($start,$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 [$start,$end].

slide_barcode

Odd - BlueFuse does not return the barcode in the file header. So it has to guess it using the data_file method guess_barcode(). Have asked the nice people at BlueGnome if they can fix this, and apparently they might, one day.

Array QC Header Information

confidence_flag_percen, confidence_flag_percen($flag)

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.

log_ratio_sd, rep_median_sd, mean_ch1_amp, mean_ch2_amp, sbr_ch1, sbr_ch2

These methods all return the relevant header information as a scalar.

Spot Information

Pass a spot index to any of these methods to retrieve the relevant value for that spot.

block_row, block_col, spot_row, spot_col

The ROW, COL, SUBGRIDROW and SUBGRIDCOL columns - describing the grid location of the spot.

feature_id, synonym_id

The NAME and ID columns - the unique identifiers of each spotted feature.

confidence, flag_id, man_excl, auto_excl

The CONFIDENCE, FLAG, MAN EXCL and AUTO EXCL columns. Flag confidence estimates can be returned separately (see above).

ch1_mean_f, ch2_mean_f, channel1_signal, channel2_signal

Actually return the AMPCH1 and AMPCH2 columns - the spot signal. The 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 channel1_signal and channel2_signal. As a result, the methods ch1_median_b and ch2_median_b are also provided in this module, but will always return '0'. However, other values for signal and background (such as snr, median_f, sd_f, mean_b and sd_b) are not returned and will generate an error.

x_pos, y_pos

The PELROW and PELCOL columns - the spot coordinates, returning the top/left position of the spot.

channel1_quality, 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

spot_diameter, uniformity, circularity, grid_offset, quality

The 2*(RADIUS), UNIFORMITY, CIRCULARITY, QUALITY and GRID OFFSET columns.

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.

TESTING

This distribution does not include a data file for testing purposes, since the one used for the test is very large. If you would like to run the full test you can download the file at http://www.instituteforwomenshealth.ucl.ac.uk/trl/pipeline/download.html.

SEE ALSO

Microarray, 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.