Dear Isaac, This is a multi-attribute link, biomart does support it. But in your specific case, I am not sure it's possible to set up since it will require ensembl mart has similar table structure as your local one, ie, two columns with affy id and chip type. I am not sure if that's the case in ensembl mart.
Best regards, Junjun Sent from my BBerry From: Isaac cano [mailto:[email protected]] Sent: Wednesday, July 20, 2011 04:16 AM To: Junjun Zhang Cc: [email protected] <[email protected]> Subject: Re: [BioMart Users] Joining Ensembl mart with a local source Dear Junjun, The local table contains this sort of rows: affyID Affy_chip 1561893_at Affy hg u133 plus 2 1564679_at Affy hg u133 plus 2 1557459_at Affy hg u133 plus 2 1565638_at Affy hg u133 plus 2 1556602_at Affy hg u133 plus 2 213515_x_at Affy hg u133 plus 2 208383_s_at Affy hg u133 plus 2 1570482_at Affy hg u133 plus 2 242772_x_at Affy hg u133 plus 2 233648_at Affy hg u133 plus 2 233073_at Affy hg u133 plus 2 244697_at Affy hg u133 plus 2 1559332_at Affy hg u133 plus 2 240992_at Affy hg u133 plus 2 1556095_at Affy hg u133 plus 2 243050_at Affy hg u133 plus 2 239606_at Affy hg u133 plus 2 1569323_at Affy hg u133 plus 2 227657_at Affy hg u133 plus 2 In this case the chip is the same for all rows so I could link to ensembl mart by the "Affy HG U133-PLUS-2" Ensembl attribute but I want to do so for future cases where the chip will be different for different affy ids. Thanks! Isaac 2011/7/20 Junjun Zhang <[email protected]<mailto:[email protected]>> Dear Isaac, Can you please show us a few rows of record in your local table so we better understand what you wanted to achieve? Thanks, Junjun Sent from my BBerry From: Isaac cano [mailto:[email protected]<mailto:[email protected]>] Sent: Wednesday, July 20, 2011 03:44 AM To: BioMart Users <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Joining Ensembl mart with a local source Dear BioMart users, I have a local database with a table containing two attributes: "gene affy Id" and "gene affy chip". I want to link this local database with the Ensembl mart in order to get, for example, the corresponding Ensembl Gene Id. I know how to add the Ensembl Gene Id attribute from the Ensembl mart by linking both sources using the "gene affy Id" local attribute and the "Affy HG U133-PLUS-2" Ensembl attribute (in this case the chip used is the Affy hg u133 plus 2). I would like to be able to link both sources in a way that the linkage is depending on the "gene affy chip" local attribute to create a more dynamic linkage. Is it possible to do it? Thanks in advance, -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]<mailto:[email protected]> -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]<mailto:[email protected]>
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