The first piece of data you are faced with is the sample. In the Workbench, a sample contains the expression values from either one array or from sequencing data of one sample. Note that the calculation of expression levels based on the raw sequence data is described in RNA-Seq analysis and Expression profiling by tags .
See more below on how to get your expression data into the Workbench as samples (under Supported array platforms).
To analyze differential expression, you need to tell the workbench how the samples are related. This is done by setting up an experiment. An experiment is essentially a set of samples which are grouped. By creating an experiment defining the relationship between the samples, it becomes possible to do statistical analysis to investigate differential expression between the groups. The Experiment is also used to accumulate calculations like t-tests and clustering because this information is closely related to the grouping of the samples.
- Supported array platforms
- Setting up an experiment
- Organization of the experiment table
- Adding annotations to an experiment
- Scatter plot view of an experiment
- Cross-view selections