I found the following issue using bioconductor annotation and I would like to hear some comment about it. The probeset 220184_at at hgu133a - affymetrix is annotated as Hs.479995 if I use the annotation package of BioConductor but if I go to netaffx(affymetrix-see details below) is annotated as Hs.329296, in both of them with Symbol: NANOG. Furthermore, using Hs.479995 in affimetrix returns no results. Maybe this is a naive question but shouldn't I suposse that the bioconductor package where created using affymetrix information ? After that I look into NCBI pages and I found that Hs.326290 is NANOG(Nanog homeobox) and Hs.479995 is NANOGP1 (Nanog homeobox pseudogene 1) and they both have the same LocusLink identifier and share some GB identifiers so, is 220184_at a probe with 2 UniGene identifier ? I appreciate any comment . Mayte if you go to netaffx: https://www.affymetrix.com/analysis/netaffx/quickquery.affx you will find the following annotation: --------------------------------------------- >From Affymetrix: 220184_at Nanog homeobox NANOG regulation of transcription, DNA-dependent transcription factor activity nucleus Probe Set ID 220184_at GeneChip Array Human Genome U133 Plus 2.0 Array Organism Common Name Human Probe Design Information Transcript ID g13376297 Sequence Type Exemplar sequence Representative Public ID NM_024865 NCBI Archival UniGene Cluster Hs.326290 NCBI -------------------------------------------- And using annaffy's functions: --------------------------------------------- aafUniGene('220184_at','hgu133a') An object of class "aafList" An object of class "aafUniGene" [1] "Hs.479995" Symbol GenBank LocusLink UniGene 220184_at NANOG NM_024865 79923 Hs.479995 -------------------------------------------------- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422

>The probeset 220184_at at hgu133a - affymetrix >is annotated as Hs.479995 if I use the annotation package of BioConductor >but if I go to netaffx(affymetrix-see details below) is annotated as >Hs.329296, in both of them with Symbol: NANOG. Furthermore, using >Hs.479995 in affimetrix returns no results. UniGene clusters change over time. Probe 220184_at was mapped to Hs.479995 in the release version but to Hs.329296 in the devel version (which was built later). To get the devel version installed you do: >library(reposTools) >install.packages2("hgu133a", develOK = TRUE) >Maybe this is a naive question but shouldn't I suposse that >the bioconductor package where created using affymetrix information ? No. The bioconductor annotation packages were created using various public data sources (e. g. LocusLink, GO, KEGG and so on). The information from Affymetrix was used to get the unified mappings between probe ids to LocusLink ids only. > >After that I look into NCBI pages and I found that >Hs.326290 is NANOG(Nanog homeobox) and Hs.479995 is NANOGP1 >(Nanog homeobox pseudogene 1) and they both have the same >LocusLink identifier and share some GB identifiers > >so, is 220184_at a probe with 2 UniGene identifier ? > >I appreciate any comment . > >Mayte > >if you go to netaffx: >https://www.affymetrix.com/analysis/netaffx/quickquery.affx >you will find the following annotation: >--------------------------------------------- >>From Affymetrix: >220184_at Nanog homeobox NANOG >regulation of transcription, DNA-dependent >transcription factor activity >nucleus >Probe Set ID 220184_at >GeneChip Array Human Genome U133 Plus 2.0 Array >Organism Common Name Human >Probe Design Information >Transcript ID g13376297 >Sequence Type Exemplar sequence >Representative Public ID NM_024865 NCBI >Archival UniGene Cluster Hs.326290 NCBI >-------------------------------------------- > >And using annaffy's functions: > >--------------------------------------------- >aafUniGene('220184_at','hgu133a') >An object of class "aafList" >An object of class "aafUniGene" >[1] "Hs.479995" > > Symbol GenBank LocusLink UniGene >220184_at NANOG NM_024865 79923 Hs.479995 >-------------------------------------------------- > > > >Mayte Suarez Farinas >The Rockefeller University >1230 York Avenue, Box 212 >New York, NY 10021 >phone: 1-212-327-8186 >fax: 1-212-327-7422 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084