I am currently converting a list of microarray probe ids to ENSEMBL IDs through biomaRt. I am currently in excel and I am seeing the same probe ID mapped to two different ENSEMBL IDs. Any idea what this means? I thought ENSEMBL IDs were based on the genes, not splicing variates or isoforms. Thanks!
Hi Scott McKay,
In the annotation process, Ensembl annotates transcripts and groups them together to form genes. We use stable IDs for all of our annotated transcripts and genes (and other annotated features too). We use ENSG# IDs for human genes, and ENST# IDs for human transcripts. There is further documentation about the stable IDs in Ensembl on the following pages:  http://www.ensembl.org/info/genome/stable_ids/index.html  http://www.ensembl.org/info/genome/stable_ids/prefixes.html
Then, Ensembl maps microarray probes to the individual transcripts of a gene: http://www.ensembl.org/info/genome/microarray_probe_set_mapping.html
Ben Ensembl Helpdesk