GenePix® Array List Examples
This page contains examples of the GenePix Array List file format, which is
documented on the GenePix File Formats
page.
Valid GAL Header Examples
Example #1 for Arrayer Software Programs
The following example shows a valid GAL file with correct header information and
useful ID (Swiss-Prot identifier) and Name content.
It is the responsibility of each arrayer manufacturer to specify relevant
information for the following header fields:
- Supplier
- ArrayerSoftwareName
- ArrayerSoftwareVersion
These fields are automatically passed to the header of the GenePix Results (GPR)
file, allowing version tracking.
Please note: the correct number of header lines must be specified in the
second line of the header or a read error will occur. For example, the following
header contains 22 lines (indicated by the blue square); the correct number is
placed in the second row of the GAL file header (indicated by the blue circle).
Example #2 for Manufacturers of Printed Microarrays
The following example shows a valid GAL file with correct header
information. A valid URL address for the Entrez protein database is
specified in the header. The ID fields contain unique protein identifiers
(Molecular Biology Database identifier = GI number).
It is the repsonsibility of each array manufacturer to supply the
relevant information for the following header fields:
- Supplier
- ArrayName
- ArrayRevision
These fields are automatically passed to the header of the GenePix Results (GPR)
file, allowing version tracking.
See Example #1 for the note on correctly specifying the number of header records.
Useful and Non-Useful Name and ID Content
GAL files specify the positions, names and meaningful ID's of the printed
substances that are deposited at each spot in the array. This information is
essential not only for the immediate image analysis needs of GenePix Pro image
analysis software but also for subsequent bioinformatics analysis.
The ID format used should be a unique identifier (UID). Examples of unique
identifiers are:
- Swiss-Prot identifier
- FlyBase identifier
- GI number (Molecular Biology Database identifier)
The accession number used in NCBI's Entrez database is NOT a unique identifier.
Please note: Name fields are not required in the GAL format. Some databases,
such as SGD, are searchable using a valid Name field (assuming correct syntax),
whereas most others public databases are not searchable using a Name field.
Important: Some identifiers (e.g., Swiss-Prot) are not unique in other
databases (e.g., Entrez). Therefore, it is important that the appropriate
URL string is included in the header section of the GAL file.
Examples of Useful Name and ID Content
| Example | Name | ID |
| NCBI Entrez Database format (GI number) | ribosomal protein S7 | 410439 |
| Swiss-Prot identifier¹ | TAS_DESSY | Q53546 |
| Blank or empty well | | empty |
| ID field only | | 40807 |
| Plate content (for Name only) | EF-TU, strain XYZ | 410439 |
¹Not a unique identifier in Entrez database.
Name fields shown in italics are not searchable parameters in the respective databases.
Examples of ID Content that are NOT Useful
| Example | Name | ID |
| No ID (the ID field must be filled) | EF-2 | |
| For a spot printed from an empty well to be automatically flagged as "Absent" by GenePix Pro, the ID field must be marked as "empty" | blank | |
| ID is not a unique identifier | | 1234 |
| Manufacturer's identifier (not unique) | | Axon 123456 |
| Multiple ID entries | EF-2 | EF2_DESMO; P33159 |
Swiss-Prot identifier used with an Entrez
URL link (not a unique identifier in Entrez) | EF-2 | P33159 |
| Plate location, example 1* | | Plate 1, Well A1 |
| Plate location, example 2* | | A1, 1 |
| Plate location, example 3* | | A-1, 1 |
| Plate location, example 4* | | Plate 1 [Plate 1], Well A1 [A1] |
* Putting plate location in the Name field is NOT useful either.
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