Affymetrix Gene Lists?

Question

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Anybody know if there is an easily accessible list to see whether genes are on a particular affymetrix microarray and associated probesets? looking through their documentation it either is not there or perhaps behind a registration wall. Thanks

Answer 1

[Kamil]

Indeed, you must register to download the files. For example, here is the page for HG-U133A 2.0. You'll probably want to look at the "Current NetAffx Annotation Files" and download one of those.

Alternatively, you can use Ensembl BioMart to get similar information -- not identical to Affymetrix. (Go to "Attributes" and then "Microarray probes/probesets".) Ensembl re-maps the probe sequences when there is a new release of the reference genome, so the reported genes assigned to probesets might be more accurate than the file provided by Affymetrix. In my experience, I find the BioMart data to be more useful (and easier to use) than the files provided by Affymetrix. I'd be interested to hear what others think about this.