NanoString nCounter Gene Expression
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      Custom Annotation Missing: How to request an import of the Probe Annotations for an nCounter Custom Codeset Panel

      Please obtain a Probe Annotation file from Nanostring, then send it to ROSALIND Support to import your Custom Panel's annotations

      Explanation:

      All genes in a Custom RLF or Custom Panel analysis will be included in the ROSALIND analysis, but may not have annotations associated with them yet. Therefore, if you see this warning but continue to upload your data then you will still see normalized expression values and differential expression results, but the Nanostring Gene Set Analysis scores or Cell Type Profiler enrichment will not be available in the analysis. 

      Resolution:

      The importing of Nanostring Custom Codeset annotations is a service provided for upgraded subscriptions and is not included with the nCounter Starter. Our subscription options can be reviewed here, but please contact sales@rosalind.bio if you have questions about upgrading. Our team would be happy to talk with you about your overall goals and make sure you have access to all of the features you need in the platform.

      Step 1:

      To have your Custom Panel annotations uploaded, please first obtain your Probe Annotations file from Nanostring. There are 2 main ways to do this:
      1. Contact bioinformatics@nanostring.com to request assistance with creating the file
      2. Create your own Probe Annotation file. For more information on creating a Probe Annotations file, please see the following article: How to Create a Probe Annotation File or refer to page 23-24 of the nCounter Advanced Analysis 2.0 User Guide.

      Step 2:

      Only ROSALIND Support can upload the Probe Annotation file for you, so once you have it please email support@rosalind.bio and provide the following 3 items:
      1. "Probe Annotations" file, it is usually is named "ProbeAnnotations_{panelName}.csv"
      2. The name you would like to use for your Custom Panel (will be visible within ROSALIND)
      3. The species used for annotation purposes

      Step 3:

      Our Support Team will then check the compatibility. Once you receive confirmation from our Support Team that these have been successfully uploaded, please proceed with uploading your data and you will notice the warning "Custom Annotation Missing" has cleared. Please contact support@rosalind.bio if you have questions or need assistance.
       
      *Note: If you are using a PanelPlus, please see here for more information.