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Hi Li, The ordering error was a problem at the BioMart server side and has now been fixed by the BioMart developers. Again thanks for reporting this error. Cheers, Steffen Li Lingdu wrote: > Hello R gurus, > > I used R "biomaRt" package to extract some annotation information about TNF > gene, > > the code I used is as below: > > ------------- > library(biomaRt) > usemaRt(biomart="ensembl",dataset="hsapiens_gene_ensembl")->en > listAttributes(mart=en,category="Structures")$name->attributes > getBM(attributes=attributes, filters="entrezgene",values=7124, > mart=en)->temp > ---------------- > > but the column names of the returned data frame is in confusion, head > information of the temp object is: > --- > struct_biotype cdna_length cds_length str_chrom_name constitutive > exon_cds_end exon_cds_start exon_chrom_end exon_chrom_start > exon_coding_end exon_coding_start rank exon_stable_id external_db_name > struct_external_gene_id gene_chrom_end gene_chrom_start gene_stable_id > peptide_length transcript_chrom_end transcript_chrom_start > transcript_chrom_strand transcript_count transcript_stable_id > translation_stable_id > 1 protein_coding 1669 702 c6_COX 1 186 1 31678370 31678016 31678370 > 31678185 1 ENSE00001495979 Uniprot/SWISSPROT TNFA_HUMAN 31680778 > 31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302 > ENSP00000372790 1 > 2 protein_coding 1669 702 c6_COX 1 232 187 31679022 31678977 31679022 > 31678977 2 ENSE00001495978 Uniprot/SWISSPROT TNFA_HUMAN 31680778 > 31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302 > ENSP00000372790 1 > 3 protein_coding 1669 702 c6_COX 1 280 233 31679257 31679210 31679257 > 31679210 3 ENSE00001495976 Uniprot/SWISSPROT TNFA_HUMAN 31680778 > 31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302 > ENSP00000372790 1 > 4 protein_coding 1669 702 c6_COX 1 702 281 31680778 31679559 31679980 > 31679559 4 ENSE00001495975 Uniprot/SWISSPROT TNFA_HUMAN 31680778 > 31678016 ENSG00000206328 233 31680778 31678016 1 ENST00000383302 > ENSP00000372790 1 > 5 protein_coding 1685 702 6 1 186 1 31651683 31651314 31651683 > 31651498 1 ENSE00001469490 HUGO TNF 31654092 31651314 ENSG00000204490 > 233 31654092 31651314 1 ENST00000376122 ENSP00000365290 1 > 6 protein_coding 1685 702 6 1 232 187 31652335 31652290 31652335 > 31652290 2 ENSE00001469486 HUGO TNF 31654092 31651314 ENSG00000204490 > 233 31654092 31651314 1 ENST00000376122 ENSP00000365290 1 > --- > > obviously, the last column is wrong. > > I think the problem happens when giving cloumn names for the retrieved > data.frame, > the order of the retrieved data.frame is not exactly the order of the > attributes. > > what happened? > > Any suggestions or helps would be greatly appreciated! > > > LiGang > > > ----- > My platform: > > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 6.0 > year 2007 > month 10 > day 03 > svn rev 43063 > language R > version.string R version 2.6.0 (2007-10-03) > > LC_COLLATE=Chinese_People's Republic of China.936; > LC_CTYPE=Chinese_People's Republic of China.936; > LC_MONETARY=Chinese_People's Republic of China.936; > LC_NUMERIC=C; > LC_TIME=Chinese_People's Republic of China.936 > --------------- > > [[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 > >