How do I determine an appropriate baseline and threshold value?
You should set these two criteria to filter and scale the raw intensity data in GRP files appropriately. We recommend you begin with the default values (baseline value of 200 and not threshold value) along with an appropriate normalization method and view the resulting “before and after” diagnostic plots to evaluate the impact of these settings. Currently, the baseline cannot be set to a value below 200 and we suggest that you use at least the minimum baseline value. Hybridizations with extremely high background and noise will require more stringent filtering than the default.
Related Questions
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- How do I determine an appropriate baseline and threshold value?
