Experimental design


In this section you specify the attributes to use for a differential expression analysis, and how samples should be compared.

Test differential expression due to

Select the attribute to test for expression effects. In figure 38, we show an example where the effects of different diets on gene expression will be tested.

Image experimentaldesign
Figure 38: Designing an experiment to test if diet affects gene expression.

You will only be able to select attributes that have values defined for all samples, and for which at least two sample groups exist.

While controlling for

This selection is optional. Use this to specify confounding factors, i.e. factors that are not of primary interest, but may affect gene expression. In figure 38, this was left as "None", but we could have selected "Gender" if we wanted to remove differences in gene expression that could be ascribed to gender.

Experimental setup (comparisons)

This selection determines the type of comparison done. Different numbers of differential expression outputs result, depending on the option selected.

Control group

If you opt for the Against control group option, you must select an attribute value to specify the control group that all remaining sample groups will be compared to.