The negative button marks wells to be negative control wells. Negative control wells are background
subtracted (if there is no standard curve), and may be used in minimum
detectable dose calculations.
Negative control wells are also known as negative wells or blank wells or "water wells" (though the contents are usually not water, but assay diluent plus particles).
To toggle negative control samples, select the samples with the mouse and click the negative button.
The Negative button acts as a toggle; each time it is clicked, the selected samples become the opposite of what they were, as shown below.
It is also possible to set negative control samples on a per-experiment level, by toggling the negative flag on the sample table for a given experiment.
As an indicator, wells are marked with a solid black bar if all the experiments using that sample treat it as a negative. The wells are marked with a small pair of bars if some experiments use it as a negative and some do not.
When using normalization, a negative sample that is not marked as such is generally undesirable in an experiment, since normalization will bring it up to the level of the other samples and make it look as if it has high levels of expression.
The use of negatives, blanks and normalization is described in the data processing document file.
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Minimum detectable dose