Normalization Button

The normalization button turns on or off normalization for a selected experiment.  

Choosing no normalizers turns off normalization entirely.
Choosing "average" normalization selects all the probes that are expressed above a threshold level.
Choose "geNorm" normalization selects probes according to the geNorm algorithm.

Normalizers can also be chosen manually, by clicking checkboxes for individual probes on the probe table.

Any change to the normalization probes (set or clear) triggers a re-computation of the data pipeline, so that the displayed data is always normalized by the set of normalization probes that are visibly checked.

The auto-selection scheme can be chosen on the top menu bar on the Settings menu.  These selected probes can be subsequently fine-tuned by hand, using the check-boxes on the probes table of the experiment.

Be aware that normalization tends to equalize differences between samples.
If there are samples with markedly different concentrations, for instance, a dilution series, normalization will bring all the wells to a single, average, dilution.
In the extreme case, if you have negative wells which are not marked as such, they will be brought up to the same level as the regular samples and will appear to have high levels of signal.
Negative wells should be marked as such.

See Also


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