
OK,
So, to sum up (and check if I understand the Human Gene ST 1.0 array), 
when summarizing to the gene level means that there are several 
probesets that compose a gene. To summarize to the gene level when 
normalizing, I executed:
OligoEset<-rma(OligoRaw,target="core")
and I got 33297 genes (transcript ids).

Using the following query on pd.hugene.1.0.st.v1:
dbListTables(conn)
dbListFields(conn,"type_dict")
info2<-"SELECT * from type_dict"
result<-dbGetQuery(conn,info2)

I got:
#  type                   type_id
#1    1                      main
#2    2             control->affx
#3    3             control->chip
#4    4 control->bgp->antigenomic
#5    5     control->bgp->genomic
#6    6            normgene->exon
#7    7          normgene->intron
#8    8  rescue->FLmRNA->unmapped

I also executed the following query:
conn<-db(pd.hugene.1.0.st.v1)
dbListTables(conn)
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 have a complete processed example (it is summarized to the gene level, 
and it has the ACC number, Symbol information, etc for each transcript 
id). I wanted to reproduce the example by myself using the raw data. 
When matching the transcript_id field given by the above query and the 
transcript_id given by the example data set, the following information 
can be extracted:

    * control->affx are related to other-spike y AFFX probe sets (57
      probe sets)
    * normgene->exon are related to 1195 pos_control probe sets
    * normgene->intron are related to 2904 neg_control probe sets

So, I suppose that there are about 4156 control transcripts.

Since I summarized to the gene level, I have used the annotation file 
"hugene10sttranscriptcluster.db". I've tried to get the ACC number and 
the Symbol for some transcript_id. The idea was to check if the results 
given were the same as the example I have. For example:

hugene10sttranscriptclusterACCNUM[["7912580"]]
I get "NM_001136561", but in the example, the accession number is 
XM_001714578. However, I get the same result for Symbol:
hugene10sttranscriptclusterSYMBOL[["7912580"]] :  LOC440563

Why are there different Accession Number for the same transcript_id?

Thanks again,
Javier

 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252  
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                 
[5] LC_TIME=Spanish_Spain.1252   

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
 [1] pd.hugene.1.0.st.v1_3.0.0            
oligoClasses_1.8.0                 
 [3] hugene10stprobeset.db_4.0.1          
hugene10sttranscriptcluster.db_4.0.1
 [5] org.Hs.eg.db_2.3.6                   
oneChannelGUI_1.12.0               
 [7] preprocessCore_1.8.0                 
GOstats_2.12.0                     
 [9] RSQLite_0.7-3                        
DBI_0.2-4                          
[11] graph_1.24.0                         
Category_2.12.0                    
[13] AnnotationDbi_1.8.0                  
tkWidgets_1.24.0                   
[15] DynDoc_1.24.0                        
widgetTools_1.24.0                 
[17] affylmGUI_1.20.0                     
affyio_1.14.0                      
[19] affy_1.24.0                          
limma_3.2.1                        
[21] Biobase_2.6.0                      

loaded via a namespace (and not attached):
 [1] annotate_1.24.0   Biostrings_2.14.0 genefilter_1.28.0 GO.db_2.3.5     
 [5] GSEABase_1.8.0    IRanges_1.4.0     RBGL_1.20.0       splines_2.10.0  
 [9] survival_2.35-7   XML_2.6-0         xtable_1.5-5    
 >


Benilton Carvalho escribió:
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>>
>>
>>
>>        [[alternative HTML version deleted]]
>>
>> <ATT00001.txt>
>
>


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