[BioC] Chromosomal positions: mapping from custom cdf file

[Hassane, Duane]

Galina,

The IDs in these remapped CDFs are UniGene IDs ... so if you parse out the numeric ID (the ID without _at and Mm.), you should be able to get that info via tools in the biomaRt package directly without going back to Affy IDs.

Regards,

Duane

_________________________________________________
Duane C. Hassane, Ph.D.
Center for Pediatric Biomedical Research
University of Rochester Medical Center
601 Elmwood Avenue, Box 703
Rochester, New York 14642

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Glazko,
Galina
Sent: Thursday, February 08, 2007 9:15 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Chromosomal positions: mapping from custom cdf file


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

 


	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor