[BioC] Human Gene ST 1.0 probeset controls

[Benilton Carvalho]

Hi Javier,

This is what you want to do:

info = dbGetQuery(conn, paste("SELECT DISTINCT meta_fsetid as  
transcript_id, type_id",
              "FROM featureSet, core_mps, type_dict",
              "WHERE featureSet.fsetid=core_mps.fsetid",
               "AND featureSet.type=type_dict.type")

I'll make sure that, in the next releases, the users are not expected  
to figure out queries like this.

Using a simplistic description: The probeset db is at the exon level;  
Transcript db is at the gene level.

b

On Nov 5, 2009, at 8:59 AM, Javier Pérez Florido wrote:

> Thanks to everybody,
> I'm new working on HuGene ST 1.0 and have some questions:
>
>    * I have normalized some CEL files using the oligo package and the
>      annotation file used, by default, is the pd.hugene.1.0.st.v1. How
>      can I access to this annotation file to check the type of control
>      probe sets used? I've tried:
>
>        conn<-db(pd.hugene.1.0.st.v1)
>        dbListTables(conn)
>        [1] "bgfeature"  "chrom_dict" "core_mps"   "featureSet"  
> "level_dict"
>        [6] "pmfeature"  "table_info" "type_dict"
>        dbListFields(conn,"featureSet")
>         [1] "fsetid"                "strand"
>        "start"                 "stop"
>         [5] "transcript_cluster_id" "exon_id"
>        "crosshyb_type"         "level"
>         [9] "chrom"                 "type"
>        sql="SELECT fsetid,type FROM featureSet"
>        dbGetQuery(conn,sql)
>        But I get integer numbers (1,2,3...) for the type field instead
>        of "AFFX*", "other-spike", etc control probe sets using the
>        annotation file....How can I get this information?
>
>    * What is the difference between hugene10stprobeset.db and
>      hugene10sttranscriptcluster.db? What is the diference between
>      summarize at the probe set level and at the gene level?
>
> Thanks again,
> Javier
> P.S. If you know any document that could help me on this arrays, it
> would be great.
>
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
> LC_MONETARY=Spanish_Spain.1252
> [4] LC_NUMERIC=C                   LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] annotate_1.24.0           AnnotationDbi_1.8.0
> pd.hugene.1.0.st.v1_3.0.0 RSQLite_0.7-3
> [5] DBI_0.2-4                 oligo_1.10.0
> preprocessCore_1.8.0      oligoClasses_1.8.0
> [9] Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0 affyio_1.14.0     Biostrings_2.14.0
> IRanges_1.4.0     splines_2.10.0    tools_2.10.0
> [7] xtable_1.5-5
>
>
> cstrato escribió:
>> Dear Javier,
>>
>> When you open the Affymetrix annotation files for the HuGene ST 1.0
>> array you will see that it does contain 13 AFFX controls and a
>> numberof "other_spike" controls for both the transcript and the
>> probeset annotation files. The MoGene array contains 22
>> "control->affx" probesets including 13 AFFX controls (bac_spike,
>> polya_spike).
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>>
>> Javier Pérez Florido wrote:
>>> Dear list,
>>> I would like to know if the GeneChip Human Gene ST 1.0 array has  
>>> some
>>> gene controls (like AFFX genes in other Affymetrix technologies).
>>> Thanks in advance,
>>> Javier
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>
>>
>>
>
>
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