Dear list, I am trying to translate mouse Entrez ids into human orthologous Entrez ids using inparanoid, and I am getting an error: > humanEGs<-inpIDMapper(tmp, srcSpecies="MUSMU", destSpecies="HOMSA", srcIDType="EG", destIDType="EG") Error in names(destIDs) = dnames : attempt to set an attribute on NULL > head(tmp) [1] "269378" "211660" "211660" "211660" "98711" "669171" (looks all right) I would be grateful if someone could indicate what I am doing wrong. Probably I missed something important about the status of INPARANOID database and AnnotationDBI? In the same time, if I am doing this via BiomaRt: tm2<-getLDS(attributes ="entrezgene",filters = "entrezgene", values = tmp, mart = mouse, attributesL = c("affy_hg_u133a","entrezgene"), martL = human) I get results and at the first glance it looks consistent. But I would prefer to use inparanoid scheme for matching orthologs... I would appreciate your help. Best regards Galina #------------------------------------------------ > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.6.0 hom.Hs.inp.db_2.4.6 org.Hs.eg.db_2.4.6 hom.Mm.inp.db_2.4.6 [5] mogene10sttranscriptcluster.db_6.0.1 mogene11stprobeset.db_2.0.2 org.Mm.eg.db_2.4.6 RSQLite_0.9-4 [9] DBI_0.2-5 AnnotationDbi_1.12.0 Biobase_2.10.0 limma_3.6.9 Confidentiality Notice: This e-mail message, including a...{{dropped:10}}

Hi Galina, This was due to a small bug in this function that prevented it from mapping to mouse IDs. The bug was caused by a change in the inparanoid mouse annotations and has been fixed in all current versions of AnnotationDbi (release and devel). You should be able to update AnnotationDbi in a day or two and benefit from the changes. Thanks for reporting this, Marc On 03/23/2011 02:14 PM, Glazko, Galina V wrote: > Dear list, > > I am trying to translate mouse Entrez ids into human orthologous Entrez ids using inparanoid, and I am getting an error: > >> humanEGs<-inpIDMapper(tmp, srcSpecies="MUSMU", destSpecies="HOMSA", srcIDType="EG", destIDType="EG") > Error in names(destIDs) = dnames : attempt to set an attribute on NULL > >> head(tmp) > [1] "269378" "211660" "211660" "211660" "98711" "669171" > (looks all right) > > I would be grateful if someone could indicate what I am doing wrong. > Probably I missed something important about the status of INPARANOID database and AnnotationDBI? > > In the same time, if I am doing this via BiomaRt: > tm2<-getLDS(attributes ="entrezgene",filters = "entrezgene", values = tmp, mart = mouse, attributesL = c("affy_hg_u133a","entrezgene"), martL = human) > > I get results and at the first glance it looks consistent. But I would prefer to use inparanoid scheme for matching orthologs... > I would appreciate your help. > > Best regards > Galina > #------------------------------------------------ >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.6.0 hom.Hs.inp.db_2.4.6 org.Hs.eg.db_2.4.6 hom.Mm.inp.db_2.4.6 > [5] mogene10sttranscriptcluster.db_6.0.1 mogene11stprobeset.db_2.0.2 org.Mm.eg.db_2.4.6 RSQLite_0.9-4 > [9] DBI_0.2-5 AnnotationDbi_1.12.0 Biobase_2.10.0 limma_3.6.9 > > > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor