[BioC] Chromosomal positions: mapping from custom cdf file

[James W. MacDonald]

Hi Galina,

Glazko, Galina wrote:
> 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.

You don't want to map back to Affy IDs. The usual mapping is _from_ Affy 
IDs to something like Entrez Gene, UniGene, RefSeq, etc. By using the 
MBNI cdf you have already mapped probes ==> genes, so you want to go 
from there.

> 
> 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,  ...

Yes. These ar UniGene IDs, with an _at added on because that is what 
MBNI tend to do. If you had googled Mm.8321 the first hit would have 
taken you here:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&term=Mm.8321

Anyway, IMO, the best thing to do from here on out is to use biomaRt to 
annotate your IDs. There are two ways you can go with biomaRt; either 
use one of the wrapper functions that Steffen has created such as 
getGene(), which will do something very similar to what you are doing 
with annaffy:

 > mart <- useMart("ensembl", "mmusculus_gene_ensembl")
Checking attributes and filters ... ok
 > getGene("Mm.8321", "unigene", mart=mart)
        ID symbol
1 Mm.8321    Cit
                                   description
1 citron [Source:MarkerSymbol;Acc:MGI:105313]
   chromosome  band strand chromosome_start
1          5 FALSE      1        116106643
   chromosome_end    ensembl_gene_id
1      116269946 ENSMUSG00000029516
   ensembl_transcript_id
1    ENSMUST00000102560

or you can use getBM() directly to get whatever annotation you might 
like. See the vignette for more information.

If you are using annaffy to create HTML tables, then you can use biomaRt 
in conjunction with the annotate package to do something very similar. 
There is a vignette that shows how to do that as well.

HTH,

Jim


> 
> Out of curiosity I googled couple of them but found nothing...
> 
>  
> 
> Thank you for your help!
> 
> Best regards
> 
> Galina
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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