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Convert Affy Id To Rs Numbers...Or Use Affy Id'S In Mach Imputation?

my goal is to perform imputation on gwas data in mach.

so, super basic question: how to convert affy SNP ids to rs numbers? i have done some online search and came up with NetAffx annotation files as the easiest solution, but that server (always) seems to be down. any workarounds/advice? an alternative (superior) solution would be to use the affy ids directly into mach, but i have seen no suggestion this is possible, and my reference genotypes are hapmap (ie, indexed by rs number). thx!

affymetrix imputation identifiers
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updated by David Quigley David Quigley • written by Occam Occam

Which Affy SNP platform are you using?

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written by Neilfws Neilfws

two old arrays - 500K & 5.0

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written by Occam Occam

1 answer

We just answered this question. I'm not sure which server you mean is always down; Affymetrix's website is reasonably reliable.

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updated by Ram Ram • written by David Quigley David Quigley

ok. that affirms the file/s i need. re: server - i was referring to the server hosting NetAffx, which i still can't access from my office network. but you are right, probably not a server issue (likely a firewall issue, will try from home). thx!

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written by Occam Occam

weirdly enough, it is actually an affy server issue. just confirmed by calling tech support.

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written by Occam Occam

I've been looking up probes today; had a 15 minute period when Netaffx refused to load, and then everything was fine. Try again, good luck.

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written by David Quigley David Quigley

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