Tech Notes

Q. How do I set up the array layout view for a chip if I have a file with a column for systematic name and 3 separate columns corresponding to probe coordinates (such as Block, Row and Column) according to how the genes are spotted on the array?

A. You will need to:

1. Create two tab-delimited text files:
   1. a specifications file (*.layout) that indicates how the probes are spotted to the chip and how coordinates are specified. You can conceivably create up to 4 specification files for each chip, one for every orientation; and
   2. a coordinates file, that indicates the gene name and corresponding coordinates in a GeneSpring-readable format.
2. Save the two generated text files to directory: SiliconGenetics/GeneSpring/data/yourGenomeName/Arraylayouts
3. Restart GeneSpring

Please refer to the GeneSpring User Manual (Section 2-13, V5.1/Feb 12/2003) for details on how to manually set up the two files to enable the Array Layout view.

Also, you can follow the instructions below to create the required files using a Microsoft ExcelŽ Macro designed to simplify file generation.

Details on creating the two tab-delimited text files:
Download the zipped ExcelŽ file. Unzip it and choose 'Enable Macros' when prompted. When you open the Excel file, you will see 4 worksheets, titled 'Sample Layout', 'Input', 'Layout' and 'Output.' On the open worksheet, 'Sample Layout', click 'Create *.layout file' to begin creation of the specifications file.

A) Create specification file: Refer to the test.layout specification settings on the 'Sample Layout' worksheet for guidance on specifying number of Vertical SubArrays, Horizontal SubArrays, columns per sub-array and rows per sub-array for your particular chip.

Next choose a name for the coordinates file you will create later.

Click on 'Generate Layout File' to use these specifications to create a file in the format required by GeneSpring. This will display the results in the 'Layout' worksheet.

Save these results as a tab-delimited file in the folder titled 'ArrayLayouts' found within the genome folder corresponding to your chip in GeneSpring/data (accessible by the desktop shortcut icon). Rather than giving the file the default ".txt" extension, save it with a ".layout" extension instead (i.e. 'mychip.layout')

B) Create coordinate file: Next, you need to paste in the tabular information that includes the column of gene names and gene coordinates in 3 separate columns as mentioned above. Click on 'Go to Input page' button. This takes you to the 'Input' worksheet'. Close the 'Layout Form' window and as per instructions on the 'Input' worksheet, copy the data containing coordinate information and paste onto the 'Input' worksheet. Click on 'Click here to create coordinate file' to get the window below.

Supply all relevant information such as the rows in which coordinate information begin and end, the column number containing the systematic gene identifier, the column number containing SubArray designation (often titled 'Block'), the column number indicating row location within a SubArray (often titled 'Row'), the column number indicating column location within a SubArray (often titled 'Column'). Then, click on 'Generate Coordinate File'. This will generate output in the 'Output' Worksheet. Close the 'Coordinate Form' window and save the results in 'Output'-worksheet by the exact name you used in the specifications file (in the window shown in Figure 1). Don't forget to save this as a tab-delimited text file in the same folder as the previous specifications file was saved (i.e. 'ArrayLayouts' folder of your genome).

Restart GeneSpring and when you open your genome window, you should now find an icon for your array layout under the 'Array Layouts' folder found in the Main Window's Navigator.