/ 
TRL-Microarray-0.063
/ TRL::Microarray::Microarray_File::BlueFuse

NAME

TRL::Microarray::Microarray_File::BlueFuse - A Perl module for managing BlueFuse 'output' files

SYNOPSIS

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

DESCRIPTION

TRL::Microarray::Microarray_File::BlueFuse is an object-oriented Perl module for managing microarray files created by 'BlueFuse' software. It inherits from TRL::Microarray::Microarray_File, and maps data fields in a BlueFuse 'output' data file to those used by TRL::Microarray::Microarray_File::Data_File.

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].

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()

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.

SEE ALSO

TRL::Microarray, TRL::Microarray::Microarray_File, TRL::Microarray::Microarray_File::Data_File

AUTHOR

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

c.jones@ucl.ac.uk

COPYRIGHT AND LICENSE

Copyright 2007 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.