On Thu, Sep 12, 2013 at 5:47 AM, Hans-Rudolf Hotz <hrh at="" fmi.ch=""> wrote: > Hi Francesco > > This is due to the actual biomart server which is access by the Bioconductor > package biomaRt. Unless, I am unaware of a recent change in the biomart > server, there is now way to preserve the order of the input (or keep > duplicates, or indicate which id does not have a result, etc). Francesco, It is an extra step, but see the match() and merge() functions to rectify your input vector with the results from biomaRt. Sean > Of course, there is a quick and dirty (and bad) solution: You loop over your > gene IDs and make an individual request for each gene.... > > > Regards, Hans-Rudolf > > > > On 09/12/2013 11:21 AM, Francesco Lescai wrote: >> >> Hi Steffen, >> thanks for your reply, yes it works this way :-) >> >> however, getBM doesn't seem to return results in the same order. here's a >> simple test >> >>> tesgenes >> >> [1] "ENSMUSG00000027255" "ENSMUSG00000020472" "ENSMUSG00000020807" >> "ENSMUSG00000086769" "ENSMUSG00000016024" >>> >>> getBM(filters=c("ensembl_gene_id"), attributes=c("ensembl_gene_id", >>> "external_gene_id"), values=tesgenes, mart=ensembl) >> >> ensembl_gene_id external_gene_id >> 1 ENSMUSG00000016024 Lbp >> 2 ENSMUSG00000020472 Zkscan17 >> 3 ENSMUSG00000020807 4933427D14Rik >> 4 ENSMUSG00000027255 Arfgap2 >> 5 ENSMUSG00000086769 Gm15587 >> >> therefore if I have a data.frame with gene IDs and I just make a cbind, it >> doesn't match. >> I solved it by merging the two data.frame by columns id like this >> >> MyResults <- merge( >> MyResults, >> getBM(filters=c("ensembl_gene_id"), attributes=c("ensembl_gene_id", >> "external_gene_id"), values= MyResults$geneID, mart=ensembl), >> by.x="geneID", >> by.y="ensembl_gene_id" >> ) >> >> is there any way to control getBM() to return data in the same order of >> the vector of values, or it is a behaviour due to the way the query works? >> >> thanks for your prompt reply, >> Francesco >> >> On 11 Sep 2013, at 17:46, Steffen Durinck >> <durinck.steffen at="" gene.com<mailto:durinck.steffen="" at="" gene.com="">> wrote: >> >> Hi Francesco, >> >> That is correct, biomaRt doesn't return anything if it can find it. It is >> designed to work just like the BioMart web services at >> www.biomart.org<http: www.biomart.org=""/> which behave the same. >> I usually add the filter as an attribute so I can match things up and >> figure out what did return a result. >> Your query would be: >> >> Anno <- >> getBM(attributes=c("affy_huex_1_0_st_v2","strand","transcript_start ","chromosome_name","hgnc_symbol"),filters=c("affy_huex_1_0_st_v2"),va lues=ID,mart=ensembl) >> >> If you want a vector back with the same length as ID and with NA's where >> you didn't get a result, you could write a wrapper function around getBM >> that does that for you. >> >> Best, >> Steffen >> >> >> On Wed, Sep 11, 2013 at 6:15 AM, Francesco Lescai >> <francesco.lescai at="" hum-gen.au.dk<mailto:francesco.lescai="" at="" hum-="" gen.au.dk="">> >> wrote: >> Hi, >> I have the same problem, and it's been this way since I used biomaRt I >> might say. >> is there any way to force getBM to return NA when the attribute >> corresponding to the filter cannot be found? >> At least when annotating your results you'd be able to get same length >> vectors, and it would be much easier to do that in data.frames. >> >> thanks for any suggestions, >> cheers, >> Francesco >> >> >> On 29 Aug 2013, at 05:40, Atul >> <atulkakrana at="" outlook.com<mailto:atulkakrana="" at="" outlook.com=""><mailto:atulkakrana at="" outlook.com<mailto:atulkakrana="" at="" outlook.com="">>> >> wrote: >> >> Hi All, >> >> I am using Oligo package to analyse samples generated using HuEx 1.0 ST v2 >> chip. The problem I am facing is with annotating the results. >> >> Here is my code (simplified): >> >> celFilesA <- list.celfiles() >> AF_data.A <- read.celfiles(celFilesA,pkgname='pd.huex.1.0.st.v2') >> AF.eset.RMA <- rma(AF_data.A,target='core') >> >>> dim(exprs(AF.eset.RMA)) >> >> [1] 22011 10 >> >> ##Attempt to annotate >> library(biomaRt) >> ID <- rownames(AF.eset.RMA) >> ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl') >> Anno <- >> getBM(attributes=c("strand","transcript_start","chromosome_name","h gnc_symbol"),filters=c("affy_huex_1_0_st_v2"),values=ID,mart=ensembl) >> >>> dim(Anno) >> >> [1] 1635 4 >> >> As you see, out of total 22011 genes/probeset I can annotate only 1635 >> genes/probesets. Is there any way I can get the annotations for all of the >> genes/probesets and add them back to my expression set (AF.eset.RMA). So, >> that annotations are included in the final results. >> >> >> Usually, with other chips I do this: >> ID <- featureNames(AF.eset.RMA) >> Symbol <- getSYMBOL(ID, 'mouse4302.db') >> Name <- as.character(lookUp(ID, "mouse4302.db", "GENENAME")) >> tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name,stringsAsFactors=F) >> tmp[tmp=="NA"] <- NA >> fData(AF.esetRMA) <- tmp >> >> And this is what I want to achieve in present case. I would appreciate >> your help. >> >> Thanks >> >> AK >> >> _______________________________________________ >> Bioconductor mailing list >> >> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""><mailto:bioconductor at="" r-project.org<mailto:bioconductor="" at="" 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org<mailto:bioconductor at="" 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]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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