Use gene information files for exon arrays in dChip:

A gene information file for exon arrays is a tab-delimited text file (with 
.XLS extension for easy opening in Excel) providing annotation information 
to transcript clusters, and have the following columns: Probe set name 
(Transcript cluster ID), Identifier (Accession number), EntrezGene 
(LocusLink ID), Gene name, Gene Ontology terms, Protein domain terms, 
Pathway terms, Chromosome terms, and Gene description.

The most frequent occurred 1200 GO terms in this array type are indexed in 
the associated "Gene Ontology.xls" file, and used as GO annotation terms in 
the gene information file. The same applies to "Protein Domain.xls". These 
two files are for fast processing of dChip.

The gene information file can be used with Affymetrix exon array gene 
expression index file which is a tab delimited data file. The first column lists the gene identifier (Transcript cluster ID) 
and each subsequent column lists the gene expression for a given sample.  At dChip, "Get External Data/Other information/Information 
files/Gene or SNP", one can specify the gene information file.  Then the gene information will be read by dChip.

In the gene information file, four annotation columns are optional: Gene 
Ontology, Protein domain, Pathway, and Chromosome terms. One can delete one 
or more of them in Excel, and save the file in tab-delimited text format. 
Also, one may replace one of these columns by custom annotation terms in a 
controlled vocabulary.