Dear Junjun, Considering that I could change the structure of our local database, I understand that I should discover how Ensembl stores the affy id and chip type information.
Thanks! Isaac 2011/7/20 Junjun Zhang <[email protected]> > 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]> > >> 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]] >> *Sent*: Wednesday, July 20, 2011 03:44 AM >> *To*: BioMart Users <[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] >> >> > > > -- > 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] > > -- 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]
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