Question

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

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12.1 years ago

Occam ▴ 410

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 • 4.5k views

ADD COMMENT • link updated 12.1 years ago by David Quigley 11k • written 12.1 years ago by Occam ▴ 410

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Which Affy SNP platform are you using?

ADD REPLY • link 12.1 years ago by Neilfws 49k

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two old arrays - 500K & 5.0

ADD REPLY • link 12.1 years ago by Occam ▴ 410

Ram · Answer 1 · 2012-04-02

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12.1 years ago

David Quigley 11k

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

ADD COMMENT • link updated 4.6 years ago by Ram 43k • written 12.1 years ago by David Quigley 11k

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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!

ADD REPLY • link 12.1 years ago by Occam ▴ 410

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

ADD REPLY • link 12.1 years ago by Occam ▴ 410

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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.

ADD REPLY • link 12.1 years ago by David Quigley 11k