The Biomedical Genomics Workbench lets you normalize expression values.

To start the normalization:

        Toolbox | Transcriptomics Analysis (Image expressionfolder)| Transformation and Normalization | Normalize (Image normalize)

Select a number of samples ( (Image array) or (Image rnaseq)) or an experiment (Image experiment) and click Next.

This will display a dialog as shown in figure 26.64.

Image normalize_step2
Figure 26.64: Choosing normalization method.

At the top, you can choose three kinds of normalization (for mathematical descriptions see [Bolstad et al., 2003]):

Figures 26.65 and 26.66 show the effect on the distribution of expression values when using scaling or quantile normalization, respectively.

Image box_plot_after_scaling_normalization_web
Figure 26.65: Box plot after scaling normalization.

Image box_plot_after_quantile_normalization_web
Figure 26.66: Box plot after quantile normalization.

At the bottom of the dialog in figure 26.64, you can select which values to normalize (see Selecting transformed and normalized values for analysis).

Clicking Next will display a dialog as shown in figure 26.67.

Image normalize_step3
Figure 26.67: Normalization settings.

The following parameters can be set:

Click Next if you wish to adjust how to handle the results. If not, click Finish.