If you can work with online conversion services, see if any of these help:

http://www.protocol-online.org/prot/Research_Tools/Online_Tools/Sequence_Analysis/Gene_ID_Conversion_Tools/

The g:Convert service (which I use once in a while myself), may do what you need.

Have you tried BioMart from Ensembl website? http://useast.ensembl.org/biomart/martview/39eef7fd1d9accfaea5f70eef7575957

Hi, thanks for the recommendations, I've tried them out, but came to a few difficulties with some of the tools:

For g:Convert - I set the target database as "ENS_HS_GENE" but all of the output becomes "NA", and I've inputted the list of Affy IDs in the query box and chose Homo Sapiens as the organism type. For the "numeric IDs treated as" section I tried both Affy options and both end up with "NA" as the output. What am I doing wrong?

For DAVID - I've only managed to make it work by converting from the OGS (official gene symbol) to Ensembl, it won't recognise my Affy IDs even if I try with all three of the Affy options in Step 2. Also, if I click on "show gene list" after they have processed my uploaded IDs, it comes up with a list that doesn't show the Ensembl ID?

For BioMart - it worked surprisingly well in terms of recognising my Affy IDs (I chose the Affy Genechip Primeview option) and did convert to Ensembl. However I had a list of 198 genes and it only outputted 170 of them, and the final table wasn't in the original order I had my genes in (also they didn't leave blanks or "NA" for the genes which they couldn't match up).

I'd be keen to use any of these three tools as long as they solve the problem, but a bit of troubleshooting is needed to overcome the difficulties! If anyone could offer advice to help, it would be much appreciated.

My experience with David personnel , they help if you write them directly

Thanks for all your answers. I ended up using BioMart which turned out to do the job quite nicely.

I had 198 Affy probes, not 198 genes, and the reason why it ended up with only 170 was because of more than one probe accounting for a gene. Just make sure you sort your gene lists in alphabetical order for the HGNC symbol in order to do the final matching check before putting the data into any analysis software.

I have the same problem. This is my first time with gene data. I'm using a data matrix from ArrayExpress. It represents some measurements of gene taken with Afflymetrix. The id used in the the rows of the matrix are not the name of the genes, and it is crazy that there is not a standard method to map Afflymetrix ids with gene names.

I tried with g-convert, but 12.000 genes out of 50.000 id have not been recognized.

I can't find on Biomart web page a tool to convert.

And David returns something, but I'm not sure it is correct, because it repeats the same id several time.

Anyone knows other methods to covert id in gene names?

Thanks,

Gabriella

Can use a R package directly to convert the gene ids..

https://support.bioconductor.org/p/23211/