Is there a consensus on how to treat the data when combining Assay and related compounds tests. We only run one related compounds and two assays per sample. Normally the related compounds results are the same for the two injections but someday they may not be. Should we average the related compounds, take the worst result, take the best result, or always report the values from the first chromatographic run. Any suggestions would be helpful

When you say "two injections" do you mean two injections from the same vial of the same preparation, or one injection from two separate vials of two preparations?

If it is two injections from the same vial/preparation, it would be acceptable to report the average, provided your injections were reproducible. However, if one of the injections appeared to be outside of any limits, it would still be advisable to perform some form of check test to confirm the results.

If it is one injection from each of two preparations DO NOT AVERAGE, when comparing results against limits - always compare BOTH results. Averaging before comparing against limits could get you in to very serious trouble with the regulatory agencies. If both results were within limits, it may be acceptable for you to report the average result on an analytical report, but you must still keep both results on file.