Tech Notes

Q. How can I perform print-tip Lowess normalization in GeneSpring?

A. The "print-tip" Lowess normalization uses a separate Lowess regression function on each print-tip region instead of the entire slide. It is referenced in the publication that can be found at: http://stat-www.berkeley.edu/users/terry/zarray/Html/normspie.html..

To perform print-tip Lowess normalization, define a column containing region designations during data loading. To do this, proceed to do the following:

1. Select "Import Data" from the File menu.
   
   
2. Select one of the files that you wish to import.
   
   
3. Select "Custom" under the "Choose File Format" pull-down menu.
   
   
4. Select the genome you wish to import your files in or create a new genome if not in the list. Click "Next".
   
   
5. In the Column Editor, assign functions to the columns that you wish to import, such as the "Gene Identifier" or "Signal" columns. For more details on how to use the Column Editor please refer to the user manual.
   
   
6. Set the column containing the region identifiers as "Region" from the Column Function pull-down menu. Click "Next" to proceed and complete the data import process.
   
   

Values in the "Region" column will be used as print-tip regions. GeneSpring will perform the Lowess normalization on a per-region basis.