Dear all, I'm working with Agilent 4X44 K human arrays. I have a vector with Agilent probenames that I would like to annotate with biomaRt. I use the following command: getBM(attributes = c("with_agilent_wholegenome", "entrezgene","wikigene_name","wikigene_description"), filters = "with_agilent_wholegenome", values = probesS, mart = ensembl) I get output, but although the vector probesS with my probe names only contains unique identifiers, biomaRt returns me identifiers with some of the identifiers replicated and which get an annotation NA. It seems like that the database is redundant. Is this possible? If not, how can I avoid this problem. Thank you for your support, Best regards, Patrick De Boever --- This e-mail, any attachments and the information it contains are confidential and meant only for the use of the addressee(s) only. Access to this e-mail by anyone other than the addressee(s) is unauthorized. If you are not the intended addressee (or responsible for delivery of the message to such person), you may not use, copy, distribute or deliver to anyone this message (or any part of its contents) or take any action in reliance on it. In such case, you should destroy this message and notify the sender immediately. If you have received this e-mail in error, please notify us immediately by e-mail or telephone and delete the e-mail from any computer. All reasonable precautions have been taken to ensure no viruses are present in this e-mail and its attachments. As our company cannot accept responsibility for any loss or damage arising from the use of this e-mail or attachments we recommend that you subject these to your virus checking procedures prior to use. [[alternative HTML version deleted]]

Hi Patrick, On 9/12/2010 3:22 PM, De Boever Patrick wrote: > Dear all, > > > I'm working with Agilent 4X44 K human arrays. I have a vector with > Agilent probenames that I would like to annotate with biomaRt. I use > the following command: > > > getBM(attributes = c("with_agilent_wholegenome", > "entrezgene","wikigene_name","wikigene_description"), filters = > "with_agilent_wholegenome", values = probesS, mart = ensembl) > > > > I get output, but although the vector probesS with my probe names > only contains unique identifiers, biomaRt returns me identifiers > with some of the identifiers replicated and which get an annotation > NA. > > It seems like that the database is redundant. Is this possible? If > not, how can I avoid this problem. The database isn't actually redundant, but it might appear to be so. Regardless, it's a simple operation to remove rows that have an NA in the second column, which will remove all your duplicates. Best, Jim > > > > Thank you for your support, > > > > Best regards, > > > > Patrick De Boever > > > --- This e-mail, any attachments and the information it contains are > confidential and meant only for the use of the addressee(s) only. > Access to this e-mail by anyone other than the addressee(s) is > unauthorized. If you are not the intended addressee (or responsible > for delivery of the message to such person), you may not use, copy, > distribute or deliver to anyone this message (or any part of its > contents) or take any action in reliance on it. In such case, you > should destroy this message and notify the sender immediately. If > you have received this e-mail in error, please notify us immediately > by e-mail or telephone and delete the e-mail from any computer. All > reasonable precautions have been taken to ensure no viruses are > present in this e-mail and its attachments. As our company cannot > accept responsibility for any loss or damage arising from the use of > this e-mail or attachments we recommend that you subject these to > your virus checking procedures prior to use. > > > > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues