NAME

Microarray::File::Data::Agilent - A Perl module for managing Agilent microarray files

SYNOPSIS

        use Microarray::File::Data::Agilent;

        my $data_file = agilent_file->new("/file.csv");

DESCRIPTION

Microarray::File::Data::Agilent is an object-oriented Perl module for managing microarray files created by Agilent Microarray Scanner software. It inherits from Microarray::File, and maps data fields in an Agilent data file to those used by Microarray::File::Data.

METHODS

Header information

The following methods return the corresponding fields from the file header;

channel1_name, channel2_name

Return 'r' and 'g' respectively.

slide_barcode

Returns 'FeatureExtractor_Barcode'.

gal_file

Returns 'FeatureExtractor_DesignFileName'.

analysis_software

This should return something about the version of the software, but at the moment just returns 'Agilent'.

scanner

Returns 'Scan_ScannerName'.

Spot data

Pass a spot index-1 to return the relevant value for the respective fields. For any method starting with 'ch1_' or 'channel1' (returning fields starting with 'r', i.e. the red channel) there is a corresponding method starting with 'ch2_' or 'channel2' (returning fields starting with 'g' i.e. the green channnel).

spot_index, spot_row, spot_col, x_pos, y_pos

The 'FeatureNum', 'Row', 'Col', 'PositionX' and 'PositionY' fields.

feature_id, synonym_id

The 'GeneName' and 'SystematicName' fields.

ch1_spot_pixels, ch1_bg_pixels

The 'rNumPix' and 'rBGNumPix' fields.

flag_id

Returns the 'IsManualFlag' field

ch1_mean_f, ch1_median_f, ch1_sd_f, ch1_mean_b, ch1_median_b, ch1_sd_b

Return the 'rMeanSignal', 'rMedianSignal', 'rPixSDev', 'rBGMeanSignal', 'rBGMedianSignal' and 'rBGPixSDev' fields.

channel1_quality, channel1_sat_pix

Return the 'rPValFeatEqBG' and 'rNumSatPix' fields.

channel1_sat

Calculates the percentage saturation for a spot, from the channel1_sat_pix() and ch1_spot_pixels() values.

channel1_signal

Returns the 'rProcessedSignal' field

channel1_snr

Calculates the signal to noise ratio as median spot signal/S.D. of the background. There's probably a field from the data file that should be used here instead. Let the author know if it bothers you!

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.