Dear list,

 

I am trying to retrieve the information about probes Chromosomal
positions (with chromosome numbers)

I used to used for that annaffy package, something like

 

library('annaffy')

probeids<-row.names(dat)

symbols <- aafSymbol(probeids, "mouse4302")

anncols <- aaf.handler()[c(1:2, 5:7,9)]

anntable <- aafTableAnn(probeids, "mouse4302", anncols)

 

but now I have custom cdf file which I got from

 

 http://brainarray.mbni.med.umich.edu
<http://brainarray.mbni.med.umich.edu/> 

 

So, instead of Affy ID's now I have another IDs which are not
recognizable by annaffy of course.

 

It might be obvious, the mapping back from these IDs to Affy's IDs, but
I am lost and do not know how to map them back.

Or, may be there is a simpler way just  to get Chr Numbers and Positions
using these new IDs directly, without intermediate step of converting
them back to Affy's?

Could someone explain this to me? IDs in my expression file now look
like this - Mm.8321_at,  ...

Out of curiosity I googled couple of them but found nothing...

 

Thank you for your help!

Best regards

Galina

 


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