Hi all,

Thanks a lot for your helps.

Wendy

2011/3/21 Hervé Pagès <hpages@fhcrc.org>

> Hi Wendy,
>
> FWIW, it seems to me that you can easily infer the mapping from
> probes to Entrez ids by combining the information stored in the
> <platform>probe and <platform>.db packages for a given platform.
>
> For example, for the hgu95av2 platform, the hgu95av2probe package
> contains the mapping between probes and probe set ids:
>
> > library(hgu95av2probe)
> > head(as.data.frame(hgu95av2probe))
>                   sequence   x   y Probe.Set.NameProbe.Interrogation.Position
> 1 TGGCTCCTGCTGAGGTCCCCTTTCC 395 301        1138_at    2631
> 2 GGCTGTGAATTCCTGTACATATTTC 322 441        1138_at    2661
> 3 GCTTCAATTCCATTATGTTTTAATG 213 419        1138_at    2703
> 4 GCCGTTTGACAGAGCATGCTCTGCG 279 435        1138_at    2781
> 5 TGACAGAGCATGCTCTGCGTTGTTG 473 299        1138_at    2787
> 6 CTCTGCGTTGTTGGTTTCACCAGCT 587 205        1138_at    2799
>  Target.Strandedness
> 1           Antisense
> 2           Antisense
> 3           Antisense
> 4           Antisense
> 5           Antisense
> 6           Antisense
>
> (Note that, unlike the probe sets, the probes don't have ids, but are
> uniquely identified by their x and y coordinates on the array.)
>
> And the hgu95av2.db package contains the mapping between probe set ids
> and Entrez ids:
>
> > library(hgu95av2.db)
> > get("1138_at", hgu95av2ENTREZID)
> [1] "6574"
> > mget(keys(hgu95av2ENTREZID)[1:5], hgu95av2ENTREZID)
> $`1000_at`
> [1] "5595"
>
> $`1001_at`
> [1] "7075"
>
> $`1002_f_at`
> [1] "1557"
>
> $`1003_s_at`
> [1] "643"
>
> $`1004_at`
> [1] "643"
>
> Cheers,
> H.
>
>
>
> On 03/15/2011 08:30 AM, Wendy Qiao wrote:
>
>> Hi all,
>>
>> I am searching for a Bioconductor package that can collapse affymetrix
>> probe
>> id to gene symbols or entrez id, but I have not had any luck yet. Does
>> anyone know any package that can collapse the probe id to gene symbols?
>>
>> Thank you in advance,
>> Wendy
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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