Genepix¨ Pro Results File Format History

http://www.moleculardevices.com/pages/software/gn_gpr_format_history.html

This page describes the various changes to the GenePix Pro Results (GPR) file format since GenePix Pro 3.0.6.

GPR files are all valid ATF files, which means that:

	- They are tab delimited text files with a single row of column titles.
	- The file header dimensions are described in the second line of the file.
	
See the GenePix Pro File Formats page for a detailed definition of the ATF format.

http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#atf


Genepix Pro 3.0.6.X/Genepix Results Format Version 1.4
This is not the original GenePix Pro Results file format, but it is the first GPR format that was widely used.


Genepix Pro 4.0.1.X/Genepix Results Format Version 2.0
The GenePix Results 2.0 format has the following differences compared to earlier versions:

	- Changed to a fixed-width four-color, three-ratio format that contains many columns of zeroes when a two-color experiment is analyzed.
	- Changed the way normalization factors are reported. Previously, factors were calculated and reported for all ratio columns, even though the GPR file was never normalized. In GenePix Pro 4.0, only the factors that are applied to the file are reported, and the factors are per wavelength normalization factors, as opposed to the per-ratio normalization factors in GenePix Pro 3.0.6.
	- Added parameters to the header, such as extra scanner parameters (e.g., scan power).
	- The analysis images had their naming convention changed.

New Columns:

	- All ratio columns were re-named on a per ratio basis, e.g., "Ratio of Medians" in GenePix Pro 3.0.6 is changed to "Ratio of Medians (635/532)". The calculation did not change.
	- Added the "Normalize" column, which is a flag column describing if the feature was used to calculate the normalization factors (1 for used, 0 for not used).


Genepix Pro 4.1.1.X/Genepix Results Format Version 3.0
From GenePix Pro 4.1, the files changed from fixed width to variable width, for two reasons:

	- GPR files now carry user-defined columns (such as annotations) that are imported from GAL files and have been carried through the analysis. GenePix Pro 4.1 allows an arbitrary number of user-defined columns, and so the GPR file has to be variable width.
	- The GPR file format continues to support three- and four-color experiments, but now contains only columns that have data in them. So a four-color GPR file from GenePix Pro 4.1 is a different width to a two-color file from GenePix Pro 4.1. The number of columns is always reported in the second line of the header.

New Columns:

	- "F635 Total Intensity" (and similar for other wavelength channels): the sum of all pixel intensities in the feature.
	- "SNR 635" (and similar for other wavelength channels): the signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean) / B635 SD.

Genepix Pro 5.0.1.X/Genepix Results Format Version 3.0
The basic file format remains the same, but with a number of new columns, and some new header rows.
New Columns:

	- "Negative Control": the Name of the negative control nearest to the feature in the same block.
	- "B635" (and similar for other wavelength channels): the actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median.
	- "F635 CV" (and similar for other wavelength channels): the coefficient of variation of feature pixel intensity.
	- "B635 CV" (and similar for other wavelength channels): the coefficient of variation of local background pixel intensity.
	- "Circularity": a measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (= p/4*100).
	- "Autoflag": reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.
	- The Sum of Means and Sum of Medians columns have changed to be on a per-ratio-channel calculation. In GenePix Pro 4.0 and 4.1, these channels summed intensities in all channels, irrespective of whether they were two-, three- or four-color experiments. Now there is a sum column for each ratio, e.g., Sum of Medians (2/1), Sum of Medians (3/1), Sum of Medians (4/1), etc., which sum the intensities for the channels in each defined ratio. For two-color experiments the calculated quantities have not changed, but the column titles have changed.
	- "Rgn R2" has been changed to "Rgn R2" wherever it occurs.

Note that the above GenePix Pro 4.1 and 5.0 GPR files are two-color files. Three- and four-color files have more columns.