Dear all: Here is some piece of output from my query: > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > getBM(attributes=c("affy_hg_u95a", "entrezgene","ensembl_transcript_id"), filters="affy_hg_u95a", values="31330_at", mart=mart) affy_hg_u95a entrezgene ensembl_transcript_id 1 31330_at 6223 ENST00000221975 2 31330_at 728953 ENST00000221975 3 31330_at 731572 ENST00000221975 I do not understand why there are multiple entrezgene ids corresponding to one affy id. Did I miss something here? Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi Weiwei, It looks like Ensembl has mapped these three entrezgene ids to the same transcript. You'll have to mail to the Ensembl helpdesk to ask why this is and to see if there is a possible error. You can reach them at: helpdesk at ensembl.org they are usually very quick to respond. Explain them what you did and what the output is (they are not familiar with the R syntax). regards, Steffen Weiwei Shi wrote: > Dear all: > > Here is some piece of output from my query: > > >> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> > Checking attributes and filters ... ok > > >> getBM(attributes=c("affy_hg_u95a", "entrezgene","ensembl_transcript_id"), filters="affy_hg_u95a", values="31330_at", mart=mart) >> > affy_hg_u95a entrezgene ensembl_transcript_id > 1 31330_at 6223 ENST00000221975 > 2 31330_at 728953 ENST00000221975 > 3 31330_at 731572 ENST00000221975 > > I do not understand why there are multiple entrezgene ids > corresponding to one affy id. Did I miss something here? > > Thanks, > >

Hi Weiwei, In my previous mail I forgot to mention that Ensembl does and independent mapping of the Affymetrix probes to the genomes and if they find multiple gene matches for one affy probe then they will display all of the matching genes. Best, Steffen Weiwei Shi wrote: > Dear all: > > Here is some piece of output from my query: > > >> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> > Checking attributes and filters ... ok > > >> getBM(attributes=c("affy_hg_u95a", "entrezgene","ensembl_transcript_id"), filters="affy_hg_u95a", values="31330_at", mart=mart) >> > affy_hg_u95a entrezgene ensembl_transcript_id > 1 31330_at 6223 ENST00000221975 > 2 31330_at 728953 ENST00000221975 > 3 31330_at 731572 ENST00000221975 > > I do not understand why there are multiple entrezgene ids > corresponding to one affy id. Did I miss something here? > > Thanks, > > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877

On Monday 02 April 2007 11:19, Weiwei Shi wrote: > Dear all: > > Here is some piece of output from my query: > > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") > > Checking attributes and filters ... ok > > > getBM(attributes=c("affy_hg_u95a", "entrezgene","ensembl_transcript_id"), > > filters="affy_hg_u95a", values="31330_at", mart=mart) > > affy_hg_u95a entrezgene ensembl_transcript_id > 1 31330_at 6223 ENST00000221975 > 2 31330_at 728953 ENST00000221975 > 3 31330_at 731572 ENST00000221975 > > I do not understand why there are multiple entrezgene ids > corresponding to one affy id. Did I miss something here? Unfortunately, this is what happens when you start mapping between identifiers defined by different authorities. If you look at the entry for ensembl transcript, you will see that it maps to three different EntrezGene IDs. Looking a bit further, you will notice that only one of them (6223) is based on a mapping between a non-predicted sequence. The other two are predicted sequences. Here is the entry in ensembl for reference: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000105372 Sean