- SEE ALSO
- COPYRIGHT AND LICENSE
Microarray::File::Data::Quantarray - A Perl module for managing Perkin Elmer 'Scanarray' microarray files
use Microarray::File::Data::Quantarray; my $data_file = quantarray_file->new("/file.csv"); my $ch1_image = quantarray_image->new("/image1.tif");
Microarray::File::Data::Quantarray is an object-oriented Perl module for managing microarray files created by Perkin Elmer's 'Scanarray' software. It inherits from Microarray::File, and maps data fields in a Scanarray data file to those used by Microarray::File::Data, as well as extracting header information from image files. The data file and image file headers that are created by Scanarray are richly annotated with a lot of useful information about your scans, allowing automated file handling that is impossible with other formats.
In case you didn't guess - where a method exists for "channel1" in the following methods, there is an equivalent method for "channel2".
Measured in micrometers.
i.e. Cyanine 3, or Cyanine 5. This comes from Scanarray's fluorochrome list, and represents whatever fluor you chose in the scan set up.
The full path of the image file when saved by Scanarray.
The full path of the GAL file, when/if imported by Scanarray during data extraction.
No idea where this comes from. But its there in the data file.
- array_columns, array_rows
Number of columns and rows of blocks on the array
- spot_columns, spot_rows
Number of columns and rows of spots in each block
And other methods that don't need any explanation;
Pass the data row index to these methods to return information for a particular spot. The first row of data is index 0.
- block_row, block_col, spot_row, spot_col, spot_index
There is no 'block number' field in Scanarray files, so all coordinates are at row/column level.
- feature_id, synonym_id
The 'Name' and 'ID' columns respectively.
- x_pos, y_pos
Spot centre location in pixels, from the top-left of the image.
You'd better look this one up... but its something like how far away the spot centre is, compared to where it was expected to be.
The flag associated with the spot.
- ch1_median_f, ch1_mean_f, ch1_sd_f
Median, mean and SD values for the fluorescence measurements of spot pixels.
- ch1_median_b, ch1_mean_b, ch1_sd_b
Median, mean and SD values for the fluorescence measurements of background pixels.
- ch1_b1sd, channel1_quality, channel1_sat
The percent of spot pixels 1 SD above background, percent of spot pixels 2 SD above background, and percent of spot pixels that are saturated.
Scanarray calculates signal to noise ratio as the median signal/background SD.
Returns the barcode, if there is only one, or if there is one at each end of the array and they are identical. Otherwise, if there are two barcodes that are different it will die with an error.
Returns the lower barcode
Returns the upper barcode
- protocol_name, protocol_id, protocol_description
These methods return details of the Scanarray protocol used to scan and extract array data
Pixel size in microns
- fluor_name, fluor_id, fluor_colour_name, fluor_description, fluor_excitation, fluor_emission
These methods return details of the fluorochrome specified in the scan protocol and visualised in this image. Not necessarily the fluorochrome used in the experiment!
- laser_id, filter_id
The Scanarray IDs of the filter and laser used in the scan
- pmt_gain, laser_power
Percentage values specified in the scan protocol
User comment can contain the slide barcode
You can change the value of a barcode in the header information. You can't overwrite the original file, but you can write these header changes to a new image file. This is achieved using the Image::ExifTool module.
my $success = $image->set_new_barcode('new barcode','/new_file.tif');
The returned values are; 1=write success, 2=write success no changes, 0=write error. If you need to change any other values, you can do by manipulating the embedded Image::ExifTool object.
my $exiftool = $image->get_exiftool_object;
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.
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.