Bad annotation file

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Bad annotation file

Postby PhilipJ » May 11 2010 9:10 am

I working with some microarray data and need to map the probes to some kind of ID (gene symbol, RefSeq, etc). The trouble is that the annotation file given to me lacks any mapping from probe sequence to ID for a huge number of probes. So, what I have is a lot of probes without identifiers. Does anybody know any good solution to this?

Of course, I could sit and run every single probe sequence through BLAST, but that would take some time. If anybody can come up with a better solution I would be very happy.
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Re: Bad annotation file

Postby mdfenko » May 11 2010 1:57 pm

agilent microarrays come with a cd with all info necessary for analysis (grid pattern, etc).

you should be able to get the information from the manufacturer if you don't have the cd.
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Re: Bad annotation file

Postby PhilipJ » May 11 2010 3:43 pm

Well, this is a custom spotted array with the OpArray probe set plus some probes of our own.
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Re: Bad annotation file

Postby mdfenko » May 12 2010 8:14 am

was it spotted in-house or by a manufacturer?

if in-house then you may be out of luck.

if by some manufacturer then they should have supplied you with a grid pattern for your analysis. get in touch with them, they will have records of custom chips they produced, even with your probes.
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