Minimum Detectable Dose

The minimum detectable dose of a target, is an estimate of the level that target should have in order to be significantly detected in a given sample.   The calculation used depends on the assay target (protein or microRNA).

Protein data

The minimum detectable dose for each probe is calculated using the negative control samples ("water wells" or "blanks") and the standard curve.

First a background value is defined as the higher of

In a perfect world, those two numbers should be the same, as the negative control wells correspond to infinite dilution, but various sources of noise introduce small differences.   Then the MDD  (in MFI units) is defined as the background plus two standard deviations of the water wells.

To calculate the MDD in protein concentration (pg/ml), the MDD in MFI is interpolated onto the standard curve.   The more negative control wells there are, the more accurate the estimate of the MDD will be.   With just two wells, the standard deviation is poorly defined, and the MDD will only be approximate.

The MDD is different for each probe.   If no negative samples are defined, no minimum detectable dose is available.

MicroRNA data

The minimum detectable dose is calculated using either negative control samples (water wells) or negative control probes (off-species probes) according to the following decision tree

Negative control samples can be selected either by selecting them on the plate view and clicking the negative button, or by checking the "neg/blank" checkbox on the Samples table.

The negative control probes are off-species microRNAs from C. elegans, A. thaliana, and O. anatinus.

If background subtraction is present (either blank probes or water wells), the MDD is adjusted for the background.

The status of MDD is shown in the experiment table.   "Probes" means that the MDD is calculated from the off-species probes.   "Water" means that the MDD is calculated from the water wells.   If any probes are marked for background subtraction, the MDD is labeled "custom".

See Also

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