How do I create a Probe Annotation file for my nCounter Custom Codeset Panel?

To create probe annotations, refer to the Advanced Analysis 2.0 User Manual for the following instructions:

  1. Get a probe annotations template. On page 21 you see the link (on the AA wizard) that you should use to get a probe annotations template. Click on “here”. (If working with custom CodeSet, you must import Probe Annotations. To upload or create probe annotations click “here”).
  2. On the next screen, select the Download CSV button and save the ProbeAnnotations.csv file to your computer. This will be your probe annotations template
  3. Modify this template file to include annotations that suit your analysis needs. The properties of each of the columns are explained in Table 1. Page 25. Column 8 has a semicolon-delimited list of annotations for each gene. The annotations  group genes in gene sets. All genes with the same annotation will be grouped for analysis. If you add an annotation on this column, ending in a semicolon you will create a new gene set. For example if you add the string: MyList; (note the semicolon) before the first annotation for each of the genes on your list (or as a first entry if there are no annotations for your gene of interest), you will see a new gene set (my list) on the advanced analysis report. Make sure to add more than 1 gene in your list. Create this way your gene sets.
  4. Save your modified template file as your new probe annotations.