Galina, It seems that there is no filter called ensembl_exon_id, the biomaRt team might be better at clarifying this or pointing you to the right filter. A workaround solution would be, ExonWithGene = getBM(c("ensembl_exon_id", ”mgi_description”,”mgi_symbol”), mart = mart) You could then merge the results with ExonWithGene. Again, the biomaRt team might get you a more elegant solution. Kind regards, Julie On 9/9/10 2:15 PM, "Glazko, Galina" wrote: Julie, yes I tried this but it did not work: > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",values=c("ENSMUSE00000844234"), mart=mart) Error in getBM(attributes = c("chromosome_name"), filters = "ensembl_exon_id", : Invalid filters(s): ensembl_exon_id Please use the function 'listFilters' to get valid filter names > I do not understand why. best regards Galina ________________________________ From: Zhu, Julie [Julie.Zhu@umassmed.edu] Sent: Thursday, September 09, 2010 2:07 PM To: Glazko, Galina; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno Galina, Since you used Exon as featureType, the feature column is the ensembl_exon_id instead of ensembl_gene ID. Kind regards, Julie On 9/9/10 1:53 PM, "Glazko, Galina" > wrote: Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_gene_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]]