Question: The adjusted negative control probe rate appears elevated, what does this mean?
Answer: The adjusted negative control probe rate measures both erroneous decoding and off-target binding, relative to the total number of high-quality transcripts detected. A high value may be due to non-specific binding, but could also be due to a low number of detected gene transcripts. The metric is an estimate of what fraction of the observed Q20 transcripts are false positives. It is important to understand that this alert does not necessarily imply that negative control probe counts are elevated (see below). Please refer to the Support Webpage for additional information on general overview of Xenium Analysis Summary metrics.
It is important to determine whether:
- The negative control probe rate appears elevated because there was an elevated number of negative control probe counts observed, indicating non-specific binding.
- The negative control probe rate appears elevated because of lower gene transcript detection.
To investigate further, see guidance in the following article:
- What is the Xenium ‘Negative control probe counts per control per cell’ metric?
- Is Xenium data usable despite a few high NCPs?
Products: Xenium In Situ Gene Expression