Affyid Mapping Without Chip Info

Question

[UnivStudent]

I have a list of affy probe IDs (e.g. 112611_at) from a microarray experiment using human samples. However, I don't have any information about what chip was used and how it corresponds with the probe IDs.

Is there anyway to map probe IDs to genes without knowledge of which chip they came from?

Answer 1

[Obi Griffith]

Check out the popular question on Gene ID conversion tool. I suggest you try bioDBnet. You can first take a set of your ids and ask it to convert from Affy ID to Affy Annotation. That will tell you which Affy platform(s) your probe sets belong to. Try enough and you should hopefully be able to narrow it down to a single platform. Then, you can convert from Affy ID to whatever type of gene ID you prefer. Or, alternatively, once you have the platform figured out you can use some of the other tools there like Ensembl BioMart.

Answer 2

[Larry_Parnell]

Affymetrix makes available (on their website) annotation files that will link the probe set IDs to gene information. You would have to try them one at a time, matching IDs to make sure that those in your list are also present in the Affy annotation file. I'd also check the positive and negative controls in your dataset to see how those match with the controls in the Affy annotation file.

Lastly, I'd see if the chip info is available from the source that gave you the data - that person or paper should have such info.

Answer 3

[Ian]

You can use DAVID to get a conversion between Affy probesets to what ever nomenclature you need as it does not require the exact array type to be displayed.