Instructions for Howto Create a GAL File
Introduction
After scanning the mArray slides, we have the quantitative information about each fluorescent spot on every slide. The quantitative information is part of what we need to perform statistical analyses on the experiment. The other piece of information that we need is a link between the name/location of the antigens spotted on the slide and the quantitative values that represent each of the antibody-antigen reactivity of the slide. The link is called a GenePix Array List (GAL) file and this document describes how to create such a file.
Preliminaries
The GAL file is a text file with specific information about the location, size, and name of each antigen spot on the slide. This file includes information that GenePix uses to create an array list. In addition, this file is necessary for creating a grid of the mArray (see Howto Grid mArray Images.doc).
This document includes the minimum requirements for creating a GAL file for probing protein mArrays. I strongly encourage the reader to review the additional literature provided below since this information will enhance and complete one’s understanding of the entire process of analyzing mArrays.
· http://www.axon.com/gn_GAL_Examples.html (an example GAL file)
· http://www.axon.com/gn_GenePix_File_Formats.html (complete details of GAL format – it’s a must read!)
· Making_GAL_Files.pdf (excellent description of how to set up a GAL file)
Entering the Proper Format
Launch Microsoft Excel
Enter all of the information in the spreadsheet (see image below). The (x, y) Features and the (x, y) Spacing come from the print setup. Note that the quotes are important.
ATF – File conforms to Axon Text File
1.0 – Version number of ATF
19 – Number of header lines (enclosed in blue rectangle)
5 – Number of data columns (Block, Column, Row, Name, ID)
“Type=GenePix ArrayList V1.0” – Type of file, same for all GAL files
“Block Count=16” – Number of blocks described in the file
“Block Type=0” – Type of block, 0 = rectangular
“BlockX=A, B, C, D, E, F, G” – The position and dimensions of each block.
A – xOrigin
B – yOrigin
C – Feature diameter
D – xFeatures (number of antigens in a row)
E – xSpacing (use spacing from the print setup)
F – yFeatures (number of antigens in a column)
G – ySpacing
Block arrangement
1 / 2 / 3 / 45 / 6 / 7 / 8
9 / 10 / 11 / 12
13 / 14 / 15 / 16
The data columns are:
Block – Block # to assign the antigen name to
Column – Column # to assign the antigen name to
Row – Row # to assign the antigen name to
Name – Antigen name
ID – pick a unique number from 1 – X (total # of antigens)
Saving the GAL file
Select File, Save As
Save the file in Excel (*.xls) format. It’s a good idea to identify the print date for the GAL file. For example, I use:
print_YY_MM_DD_array_list_for_gal.xls
Select File, Save As
Save the file in text (Tab delimited)(*.txt) format. For example:
print_YY_MM_DD_array_list_for_gal.txt
Excel will complain about multiple sheets. Click OK. Excel will now complain about containing features that are not compatible with Text. Click Yes.
Select File, Close (or Exit)
Excel will ask about saving changes. Click No and Excel will end.
Editing the Text file
Launch Notepad
Select File, Open…
Find the GAL file in the *.txt format.
Change all the triple quotes (“””) to single quotes (“).
Select File, Save
Select File, Exit
Launch Windows Explorer
Change the folder options to show the file extensions
Select Tools, Folder Options…
Select the View Tab
Uncheck the box Hide file extensions for known file types
Select OK
Find the GAL file in the *.txt format
Create a copy of the print_YY_MM_DD_array_list_for_gal.txt
Right click on the print_YY_MM_DD_array_list_for_gal.txt file and rename it as:
print_YY_MM_DD_array_list_for_gal.gal
Windows may complain about the file extension being unstable of unusable. Select Yes.
Now the GAL file is formatted and ready to use!