## Outline of expression data analysis

The data analysis steps that are essentially needed before anything else can be accomplished are importing the data, normalizing it, and describing the experimental setup, i.e., filling in the phenodata. This set of analysis does not yield any interesting results, so probably you also want run at least some filtering or statistical testing steps in order to generate some gene lists from which to continue the wet-lab experimentation. So, in one possible order from the beginning to the end of the analysis, the steps could be:

- Read in raw data
- Normalize
- Fill in the phenodata
- Do quality control (optional)
- Filter genes (optional)
- Run statistical tests (optional)
- Cluster the genes and samples (optional)
- Annotate the results (optional)
- Save and export the data (optional)

For more information about each of the steps, please see CSC's DNA microarray data analysis -book.