A candidate FAQ to Chapter 28. Reporters related FAQs
This siutation should be covered in the FAQ:
In some cases the reporter annotation file from Affymetrix fails to describe all probe sets on the chip, you may get a message like Error: Unable to import root bioassay. Item not found: Reporter[externalId=AFFX-2315060]. In this case you have to fall back to importing the probe set information using the CDF file, simply do
Import the reporters by choosing 'View' -> 'Reporters' and the clicking on 'Import...'. Click 'Next' without changing the 'auto detect' settings. Supply the CDF file name in the next dialog, click 'Next'. Start the import by clicking 'Next' in the parameter dialog. This will add the missing probe sets without changing existing probe sets. The new probe sets will not have any annotations associated with them since the CDFs do not contain such information.
This is already somewhat highlighted in the Array LIMS chapter but the text is not completely clear and should be rewritten.