[BioC] mapping probe sets from yeast2 array to probe sets in hgu133A

[James W. MacDonald]

  Hi Galina,

The trivial step is converting from yeast2 probe IDs to say, ENSEMBL 
IDs, and then converting e.g., Entrez Gene IDs to hgu133a probe IDs.

But you seem lost, so here is a full example:

 > library(yeast2.db)
 > ids <- Rkeys(yeast2ENSEMBL) ## you could use other ids as well, I suppose
 > length(ids)
[1] 5883
 > egids <- idConverter(ids, "SACCE","HOMSA","ENSEMBL")
Loading required package: hom.Sc.inp.db
Loading required package: org.Hs.eg.db
 > length(egids)
[1] 1505
 > class(egids)
[1] "list"
 > table(sapply(egids, length))

    1    2    3   13
1459   41    4    1

## so 1505 things were converted, most 1-1.

 > library(hgu133a.db)
 > hguids <- mget(unlist(egids), revmap(hgu133aENTREZID))
 > length(hguids)
[1] 1566
 > table(sapply(hguids, length))

    1    2    3    4    5    6    7    9
1040  303  147   54   16    4    1    1
 > hguids[1:10]
$`4512`
[1] NA

$`4508`
[1] NA

$`4519`
[1] NA

$`4513`
[1] NA

$`100289404`
[1] NA

$`100292744`
[1] NA

$`23355`
[1] "209553_at"

$`3312`
[1] "208687_x_at" "210338_s_at" "221891_x_at"

$`4913`
[1] "209731_at"

$`5519`
[1] "202883_s_at" "202884_s_at" "202885_s_at" "202886_s_at" "222351_at"

So this will give you all the homologous probesets on the HGU133a chip. 
If you want to know which yeast2 probeset ID maps to a given HGU133a 
probeset, you will have to do some extra work tracking the names.

Best,

Jim



On 8/6/10 2:06 PM, Glazko, Galina wrote:
> Jim,
>
> Thank you for the answer.
> I would appreciate if you could describe the 'trivial' step:
> "converting from yeast2 probe IDs to hgu133a probe IDs"?
> It is not obvious for me, sorry.
>
> Best regards
> Galina
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Friday, August 06, 2010 12:10 PM
> To: Glazko, Galina
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] mapping probe sets from yeast2 array to probe sets in hgu133A
>
>    Hi Galina,
>
> See ?idConverter in the AnnotationDbi package. You will have to do some
> extra work converting from yeast2 probe IDs to hgu133a probe IDs, but
> that is trivial.
>
> Best,
>
> Jim
>
>
>
> On 8/5/10 2:42 PM, Glazko, Galina wrote:
>> Dear List,
>>
>> I would appreciate if someone could indicate the easy way how to map probe
>> sets from yeast2 array onto hgu133a probe sets in Bioconductor;
>> May be throughout BioMart?
>> (Mapping should be based on orthologs).
>>
>> I know how to do it in NetAffx, Affymetrix but it takes too much time.
>> Thank you!
>>
>> Best regards
>> Galina
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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