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).
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
- the bottom asymptote of the standard curve
- the mean of the negative control wells
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.
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
- If off-species probes are available
- calculate a single MDD for all probes using the mean+3 standard deviation of the off-species probes across all wells. E.g. if there are 3 off-species probes and 64 samples, 192 data points are used.
- If water wells are also available,
- If more than 10% of the probes in the water wells are above the MDD just calculated, recalculate an MDD for each probe using the mean + 3 standard deviation of each probe in the water wells
- Else continue using the MDD calculated from the off-species probes
- If water wells are available,
- calculate MDD for each probe using the mean + 3 standard deviation of each probe in the water wells
- Otherwise, no MDD is calculated
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".
Help Front Page