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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