## Annotation / Affymetrix, Illumina or Agilent gene list

### Description

This tool creates an HTML page containing annotations for a selected Affymetrix, Illumina or Agilent gene list.

### Parameters

- Column containing expression values [empty]
- Column containing p-values [empty]

### Details

Currently, Affymetrix probe set IDs, Illumina Target IDs and Agilent probe names can be annotated. Note that if a gene is annotated with several terms of the same branch in the Gene Ontology (GO) hierarchy, (e.g. Regulation of cell death / Regulation of programmed cell death / Regulation of apoptotic process), this tool will list only the most specific term and the parent terms are ignored. If you would like to list all the terms, please use the tool "Annotation / Add annotations to data" so that you set the parameter Conditional to yes.

If the dataset contains p-values or expression values, these can be included in the annotation table. P-values and expression values can be calculated using statistical tests, especially empirical Bayes, or using the tool "Utilities / Calculate fold change".

### Output

Tool writes an HTML and a text file with annotations for the genes. This annotation page contains information on the probe location in the chromosomes, links to outside databases, such as, Pubmed and RefSeq, and GO and KEGG pathway information.

### References

This tool utilizes the Bioconductor package annaffy.