Control Gene Normalization

Use this option to specify which control gene normalization method to use, Positive Control, Negative Control, or None.

Positive Control normalization, also known as code-count normalization, uses a series of exogenous probes (genes) of known concentration. Observed variation for these genes can be attributed specifically to the assay. Normalization occurs by summarizing (i.e. mean or geometric mean) the positive control counts and adjusting samples by a factor relative to other samples.

In Negative Control normalization, also known as background correction, the background level is calculated as an aggregate summary of six to eight control probes with no target transcript. The calculated background level for each sample is then subtracted from the adjusted probe value.

Both methods are used to deal with the variation specifically attributed to the assay itself, but from different perspectives. Choosing either of them should enable you to correct for assay variation, depending on the conditions of your analysis. Because neither method has been proven to work best in all situations or study designs, you should consider doing multiple runs using different methods and compare the outcomes.

Choose None when you opt to use non-normalized data.