Global Lowess Normalisation

1. Click the button

2. Click the Normalization button.

3. Click the Global Lowess button.

4. Set the Plot Type to log

5. Click plot

The left window is the un-normalized data, the blue line is the normalization line and the left window is the normalized data

5. Click OK

Quantile Normalisation

Quantile normalisation (Bolstad et al 2002) makes different arrays comparable by making sure that the distribution of intensities are the same across arrays. The normalisation distribution is chosen by averaging each quantile across chips.

1. In the Data tab, when Data Source Type is set to AB1700 or Tabular, there is a check box in the middle of the page named Quantile normalize all arrays. For the Tabular data source type, Singel Channel must be checked before Quantile normalize all arrays becomes active. Check this box to perform quantile normalisation when the data is imported.