yes. everything, but the Prof part, is correct. ;) b On Nov 9, 2009, at 1:17 PM, Javier P?rez Florido wrote: > Thanks Prof. Carvalho, > Is the rest of my e-mail correct? > Thanks, > Javier > > > Benilton Carvalho escribi?: >> XM_001714578 was replaced by NM_001136561. >> >> http://www.ncbi.nlm.nih.gov/nuccore/NM_001136561?log$=seqview_status >> >> b >> >> On Nov 9, 2009, at 9:19 AM, Javier P?rez Florido wrote: >> >>> >>> 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 escribi?: >>>> >>>> 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 P?rez 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 escribi?: >>>>>> 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 P?rez 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 at 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> >>>> >>>> >>> >> >> >