error with retrieving dn and ds using biomart

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lemon tree ▴ 40

@lemon-tree-5473

Last seen 10.2 years ago

Dear All, I have a list of human genes with EntrezGene IDs. And I want to retrieve dN and dS values of them from biomaRt. I used the following command. library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") inputfile<-"gene_list.txt"; geneIDs<-read.table(inputfile,header=F); dnds <- getBM(attributes = c("entrezgene", "mmusculus_homolog_dn", "mmusculus_homolog_ds"), filters = c("entrezgene"), values= geneIDs, mart = ensembl) There is an error as the following: Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Could anyone give some suggestions on this? Thanks very much! Best all! -- David Wang [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.7 years ago by James W. MacDonald 67k • written 11.7 years ago by lemon tree ▴ 40

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 days ago

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Hi David, On 3/19/13 12:26 PM, David Wang wrote: > Dear All, > I have a list of human genes with EntrezGene IDs. And I want to > retrieve dN and dS values of them from biomaRt. > I used the following command. > library(biomaRt) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > inputfile<-"gene_list.txt"; > geneIDs<-read.table(inputfile,header=F); > dnds <- getBM(attributes = c("entrezgene", "mmusculus_homolog_dn", > "mmusculus_homolog_ds"), filters = c("entrezgene"), values= geneIDs, mart = > ensembl) > There is an error as the following: > Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple > attribute pages are not allowed There are certain attribute pages on the Biomart server, and you cannot get data from more than one. > x <- listAttributes(mart, what=c("name","description","page")) > x[x[,1] %in% c("entrezgene","mmusculus_homolog_dn","mmusculus_homolog_ds"),] name description page 47 entrezgene EntrezGene ID feature_page 577 mmusculus_homolog_dn dN homologs 578 mmusculus_homolog_ds dS homologs So the homolog data you want come from the homologs page, but the entrezgene data come from the feature_page, hence you cannot get all three at one time. Best, Jim > > Could anyone give some suggestions on this? Thanks very much! > > Best all! >

ADD COMMENT • link 11.7 years ago James W. MacDonald 67k

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Dear Jim and all, Thank you! I have changed the EntrezGene IDs to ensembl IDs to redo it. A simple example is as the following: dnds <- getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn","mmusculus_homolog_ds"), filters = "ensembl_gene_id", values = "ENSG00000139618", mart = mart) But there is an error as the following: Error in `[.data.frame`(result, , attributes) : undefined columns selected Could you give me some suggestion about this? Thank you very much! On Tue, Mar 19, 2013 at 12:03 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi David, > > > > On 3/19/13 12:26 PM, David Wang wrote: > There are certain attribute pages on the Biomart server, and you cannot > get data from more than one. > > > x <- listAttributes(mart, what=c("name","description","**page")) > > x[x[,1] %in% c("entrezgene","mmusculus_**homolog_dn","mmusculus_** > homolog_ds"),] > name description page > 47 entrezgene EntrezGene ID feature_page > 577 mmusculus_homolog_dn dN homologs > 578 mmusculus_homolog_ds dS homologs > > So the homolog data you want come from the homologs page, but the > entrezgene data come from the feature_page, hence you cannot get all three > at one time. > > Best, > > Jim > > > -- David Wang [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago lemon tree ▴ 40

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I have 18 RNAseq libraries for 9 samples in duplicate. When I generated edgeR object, I found all the norm.factors are 1 even though the library size are so different. Could anyone please explain this for me and let me know if it is correct? Thanks. Here are the code some results: > group=factor(substring(names, 1,2)) > group [1] MP FA FR FW MA FW MM FP MA MW FM MM MW MP MM FP FA FR Levels: FA FM FP FR FW MA MM MP MW > design=model.matrix(~0+group) > y=DGEList(counts=data.used, group=group) Calculating library sizes from column totals. > y An object of class "DGEList" $counts MP FA FR FW MA FW.1 MM FP MA.1 MW FM MM.1 MW.1 MP.1 MM.2 FP.1 GS_14929 221 284 170 23 267 105 209 106 52 218 158 277 170 926 185 211 GS_09776 75 32 17 28 41 96 86 15 23 65 23 27 65 73 87 85 GS_18434 36 22 19 8 21 6 22 7 7 27 13 6 21 2 23 15 GS_08334 44 77 23 50 41 78 78 14 21 61 29 8 46 59 94 132 GS_09550 82 92 45 54 105 75 95 18 79 153 41 8 111 11 86 178 FA.1 FR.1 GS_14929 159 0 GS_09776 52 143 GS_18434 14 23 GS_08334 92 60 GS_09550 97 39 15457 more rows ... $samples group lib.size norm.factors MP MP 2220863 1 FA FA 2179157 1 FR FR 1181036 1 FW FW 1305802 1 MA MA 1780507 1 13 more rows ... > y$samples group lib.size norm.factors MP MP 2220863 1 FA FA 2179157 1 FR FR 1181036 1 FW FW 1305802 1 MA MA 1780507 1 FW.1 FW 3388037 1 MM MM 2564495 1 FP FP 749402 1 MA.1 MA 1299287 1 MW MW 2579787 1 FM FM 1355962 1 MM.1 MM 867100 1 MW.1 MW 2581031 1 MP.1 MP 2115532 1 MM.2 MM 2869116 1 FP.1 FP 3112223 1 FA.1 FA 2715113 1 FR.1 FR 2770152 1 ------------------------- Here I can see, MP lib.size is 2220863, wherease FP lib.size is only 749402, but both norm.factors are 1 I am very confused... [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago capricy gao ▴ 230

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Hi Caprice, Probably you also want to run: y <- calcNormFactors(y) ? then have a look at y$samples ? Best, Mark On 19.03.2013, at 22:38, capricy gao <capricyg at="" yahoo.com=""> wrote: > I have 18 RNAseq libraries for 9 samples in duplicate. When I generated edgeR object, I found all the norm.factors are 1 even though the library size are so different. Could anyone please explain this for me and let me know if it is correct? Thanks. > > Here are the code some results: > >> group=factor(substring(names, 1,2)) >> group > [1] MP FA FR FW MA FW MM FP MA MW FM MM MW MP MM FP FA FR > Levels: FA FM FP FR FW MA MM MP MW >> design=model.matrix(~0+group) >> y=DGEList(counts=data.used, group=group) > Calculating library sizes from column totals. >> y > An object of class "DGEList" > $counts > MP FA FR FW MA FW.1 MM FP MA.1 MW FM MM.1 MW.1 MP.1 MM.2 FP.1 > GS_14929 221 284 170 23 267 105 209 106 52 218 158 277 170 926 185 211 > GS_09776 75 32 17 28 41 96 86 15 23 65 23 27 65 73 87 85 > GS_18434 36 22 19 8 21 6 22 7 7 27 13 6 21 2 23 15 > GS_08334 44 77 23 50 41 78 78 14 21 61 29 8 46 59 94 132 > GS_09550 82 92 45 54 105 75 95 18 79 153 41 8 111 11 86 178 > FA.1 FR.1 > GS_14929 159 0 > GS_09776 52 143 > GS_18434 14 23 > GS_08334 92 60 > GS_09550 97 39 > 15457 more rows ... > > $samples > group lib.size norm.factors > MP MP 2220863 1 > FA FA 2179157 1 > FR FR 1181036 1 > FW FW 1305802 1 > MA MA 1780507 1 > 13 more rows ... > >> y$samples > group lib.size norm.factors > MP MP 2220863 1 > FA FA 2179157 1 > FR FR 1181036 1 > FW FW 1305802 1 > MA MA 1780507 1 > FW.1 FW 3388037 1 > MM MM 2564495 1 > FP FP 749402 1 > MA.1 MA 1299287 1 > MW MW 2579787 1 > FM FM 1355962 1 > MM.1 MM 867100 1 > MW.1 MW 2581031 1 > MP.1 MP 2115532 1 > MM.2 MM 2869116 1 > FP.1 FP 3112223 1 > FA.1 FA 2715113 1 > FR.1 FR 2770152 1 > ------------------------- > Here I can see, MP lib.size is 2220863, wherease FP lib.size is only 749402, but both norm.factors are 1 > > I am very confused... > [[alternative HTML version deleted]] > > _______________________________________________ > 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

ADD REPLY • link 11.7 years ago Mark Robinson ▴ 880

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Geez, I forgot it. Thanks a lot!! ________________________________ From: Mark Robinson <mark.robinson@imls.uzh.ch> Cc: "Bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Tuesday, March 19, 2013 4:48 PM Subject: Re: [BioC] edgeR strange normalized factor for RNAseq data Hi Caprice, Probably you also want to run: y <- calcNormFactors(y) … then have a look at y$samples … Best, Mark > I have 18 RNAseq libraries for 9 samples in duplicate. When I generated edgeR object, I found all the norm.factors are 1 even though the library size are so different. Could anyone please explain this for me and let me know if it is correct? Thanks. > > Here are the code some results: > >> group=factor(substring(names, 1,2)) >> group > [1] MP FA FR FW MA FW MM FP MA MW FM MM MW MP MM FP FA FR > Levels: FA FM FP FR FW MA MM MP MW >> design=model.matrix(~0+group) >> y=DGEList(counts=data.used, group=group) > Calculating library sizes from column totals. >> y > An object of class "DGEList" > $counts > MP FA FR FW MA FW.1 MM FP MA.1 MW FM MM.1 MW.1 MP.1 MM.2 FP.1 > GS_14929 221 284 170 23 267 105 209 106 52 218 158 277 170 926 185 211 > GS_09776 75 32 17 28 41 96 86 15 23 65 23 27 65 73 87 85 > GS_18434 36 22 19 8 21 6 22 7 7 27 13 6 21 2 23 15 > GS_08334 44 77 23 50 41 78 78 14 21 61 29 8 46 59 94 132 > GS_09550 82 92 45 54 105 75 95 18 79 153 41 8 111 11 86 178 > FA.1 FR.1 > GS_14929 159 0 > GS_09776 52 143 > GS_18434 14 23 > GS_08334 92 60 > GS_09550 97 39 > 15457 more rows ... > > $samples > group lib.size norm.factors > MP MP 2220863 1 > FA FA 2179157 1 > FR FR 1181036 1 > FW FW 1305802 1 > MA MA 1780507 1 > 13 more rows ... > >> y$samples > group lib.size norm.factors > MP MP 2220863 1 > FA FA 2179157 1 > FR FR 1181036 1 > FW FW 1305802 1 > MA MA 1780507 1 > FW.1 FW 3388037 1 > MM MM 2564495 1 > FP FP 749402 1 > MA.1 MA 1299287 1 > MW MW 2579787 1 > FM FM 1355962 1 > MM.1 MM 867100 1 > MW.1 MW 2581031 1 > MP.1 MP 2115532 1 > MM.2 MM 2869116 1 > FP.1 FP 3112223 1 > FA.1 FA 2715113 1 > FR.1 FR 2770152 1 > ------------------------- > Here I can see, MP lib.size is 2220863, wherease FP lib.size is only 749402, but both norm.factors are 1 > > I am very confused... > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago capricy gao ▴ 230

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Hi David, Apparently the Biomart server is doing something crazy and returning Alpaca homologs. You can see this if you first do options(error=recover) dnds <- getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn"," mmusculus_homolog_ds"), filters = "ensembl_gene_id", values = ensgs, mart = mart) and then you will see something like > getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn","mmusculus_homolog_ds"), filters = "ensembl_gene_id", values = ensgs, mart = mart) Error in `[.data.frame`(result, , attributes) : undefined columns selected Enter a frame number, or 0 to exit 1: getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn", "mmusculus_ 2: result[, attributes] 3: `[.data.frame`(result, , attributes) If you choose 2, you will enter the debugger at that point and can then do something like Browse[1]> head(result) ensembl_gene_id vpacos_homolog_dn vpacos_homolog_ds 1 ENSG00000114786 0.1161 0.5425 2 ENSG00000125954 NA NA 3 ENSG00000159403 0.1330 0.6510 4 ENSG00000251246 0.0765 0.6598 5 ENSG00000255730 NA NA 6 ENSG00000256349 0.0536 0.6109 and then if you grep vpacos in the results from listAttributes, you can see that these are Alpaca homologs. Or at least the header indicates that. So either Steffen Durinck or somebody at Ensembl will have to look into this, as I am now officially out of my depth. Best, Jim On Tue, Mar 19, 2013 at 2:22 PM, David Wang <lemon.wang218@gmail.com> wrote: > Dear Jim and all, > Thank you! I have changed the EntrezGene IDs to ensembl IDs to redo > it. A simple example is as the following: > dnds <- getBM(attributes = c("ensembl_gene_id", > "mmusculus_homolog_dn","mmusculus_homolog_ds"), filters = > "ensembl_gene_id", values = "ENSG00000139618", mart = mart) > But there is an error as the following: > Error in `[.data.frame`(result, , attributes) : > undefined columns selected > > Could you give me some suggestion about this? Thank you very much! > > On Tue, Mar 19, 2013 at 12:03 PM, James W. MacDonald <jmacdon@uw.edu>wrote: > >> Hi David, >> >> >> >> On 3/19/13 12:26 PM, David Wang wrote: >> There are certain attribute pages on the Biomart server, and you cannot >> get data from more than one. >> >> > x <- listAttributes(mart, what=c("name","description","**page")) >> > x[x[,1] %in% c("entrezgene","mmusculus_**homolog_dn","mmusculus_** >> homolog_ds"),] >> name description page >> 47 entrezgene EntrezGene ID feature_page >> 577 mmusculus_homolog_dn dN homologs >> 578 mmusculus_homolog_ds dS homologs >> >> So the homolog data you want come from the homologs page, but the >> entrezgene data come from the feature_page, hence you cannot get all three >> at one time. >> >> Best, >> >> Jim >> >> >> -- > David Wang > [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago James W. MacDonald 67k

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Dear David, I have tried the following queries on an out of date R and biomaRt and I got the mouse dn and ds values back: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", "hsapiens_gene_ensembl") dnds <- getBM(attributes = c("ensembl_gene_id","mmusculus_homolog_dn","mmusculus_homolog_ds"), filters ="ensembl_gene_id", values = "ENSG00000139618", mart = mart) I have just updated R to 2.15.3 and BiomaRt to 2.14.0 and I am now getting the following error back: Error in `[.data.frame`(result, , attributes) : undefined columns selected This might be coming from the latest version of BiomaRt. Hope this helps, Thomas On 19 Mar 2013, at 20:56, James W. MacDonald wrote: > Hi David, > > Apparently the Biomart server is doing something crazy and returning Alpaca > homologs. You can see this if you first do > > options(error=recover) > dnds <- getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn"," > mmusculus_homolog_ds"), filters = "ensembl_gene_id", values = ensgs, mart = > mart) > > and then you will see something like > >> getBM(attributes = c("ensembl_gene_id", > "mmusculus_homolog_dn","mmusculus_homolog_ds"), filters = > "ensembl_gene_id", values = ensgs, mart = mart) > Error in `[.data.frame`(result, , attributes) : > undefined columns selected > > Enter a frame number, or 0 to exit > > 1: getBM(attributes = c("ensembl_gene_id", "mmusculus_homolog_dn", > "mmusculus_ > 2: result[, attributes] > 3: `[.data.frame`(result, , attributes) > > If you choose 2, you will enter the debugger at that point and can then do > something like > > Browse[1]> head(result) > ensembl_gene_id vpacos_homolog_dn vpacos_homolog_ds > 1 ENSG00000114786 0.1161 0.5425 > 2 ENSG00000125954 NA NA > 3 ENSG00000159403 0.1330 0.6510 > 4 ENSG00000251246 0.0765 0.6598 > 5 ENSG00000255730 NA NA > 6 ENSG00000256349 0.0536 0.6109 > > and then if you grep vpacos in the results from listAttributes, you can see > that these are Alpaca homologs. Or at least the header indicates that. > > So either Steffen Durinck or somebody at Ensembl will have to look into > this, as I am now officially out of my depth. > > Best, > > Jim > > > > > > On Tue, Mar 19, 2013 at 2:22 PM, David Wang <lemon.wang218@gmail.com> wrote: > >> Dear Jim and all, >> Thank you! I have changed the EntrezGene IDs to ensembl IDs to redo >> it. A simple example is as the following: >> dnds <- getBM(attributes = c("ensembl_gene_id", >> "mmusculus_homolog_dn","mmusculus_homolog_ds"), filters = >> "ensembl_gene_id", values = "ENSG00000139618", mart = mart) >> But there is an error as the following: >> Error in `[.data.frame`(result, , attributes) : >> undefined columns selected >> >> Could you give me some suggestion about this? Thank you very much! >> >> On Tue, Mar 19, 2013 at 12:03 PM, James W. MacDonald <jmacdon@uw.edu>wrote: >> >>> Hi David, >>> >>> >>> >>> On 3/19/13 12:26 PM, David Wang wrote: >>> There are certain attribute pages on the Biomart server, and you cannot >>> get data from more than one. >>> >>>> x <- listAttributes(mart, what=c("name","description","**page")) >>>> x[x[,1] %in% c("entrezgene","mmusculus_**homolog_dn","mmusculus_** >>> homolog_ds"),] >>> name description page >>> 47 entrezgene EntrezGene ID feature_page >>> 577 mmusculus_homolog_dn dN homologs >>> 578 mmusculus_homolog_ds dS homologs >>> >>> So the homolog data you want come from the homologs page, but the >>> entrezgene data come from the feature_page, hence you cannot get all three >>> at one time. >>> >>> Best, >>> >>> Jim >>> >>> >>> -- >> David Wang >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago Thomas Maurel ▴ 800

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