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Viewing Experimental Designs

An “experimental design” describes the characteristics of each sample as is relevant to the analysis of the experiment. Experimental designs are not populated for all studies, as this has to be done manually in many cases. Some studies were annotated by GEO curators and those annotations appear in Gemma.

Getting to the page: To find the experimental design page, select your data set of interest from the dataset (expression experiment) browser. Then click on the Experimental Design tab at the top of the page. From here, you can click the Show Details icon which will take you to the Experimental Design Details page. The two tabs on this page are Design Setup, which provides the experimental factors and factor values used (For definitions, see the Glossary page. For more detailed descriptions of factors and factor values visit the Editing Experimental Designs page.) and Sample Details, which provides a complete list of the samples in the study and the parameters that apply to each sample.

About experimental designs
An experimental design (ED) is organized around experimental factors (EFs), listed near the top of the page. A factor is a known variable in an experiment, such as “age”, “genotype” or “treatment”. An experiment can have any number of factors, but most have only 1-3.

Each sample has a specific Factor Value (FV) for each Factor. For example, for ‘genotype’, the available values might be “wild-type” and “mutant”. The available factor values for a given EF are shown in the middle of the page. For a parameter like “age”, the values might be continuous values (numbers) like “10.1 years”.

Because experimental designs are curated manually (either by us or by the original source, such as GEO), it is certainly possible for errors to exist. If you spot a problem, please contact gemma@chibi.ubc.ca.

Editing experimental designs
If the data set is yours, or you are an administrator on the system, you can edit or create experimental designs. Visit the page on Experimental Design Editing.