On Tue, May 11, 2010 at 2:15 AM, varpal singh <gilvarpal@gmail.com> wrote: > Hi Sir,, > > I would like to know about entrez id of arabidopsis, I have probe ids of > differential expressed genes, I wan to know about their entrez id by > bioconductor, how van i get?? > Please tell me!! > > Hi, Varpal. Please write to the bioconductor email list when asking questions. You will get better answers there and many people can benefit from those answers. As to your question, you'll need to be more specific about what you have done. In particular, what array are you using? Also, when asking questions on the list, be sure to include the output of sessionInfo(). Sean [[alternative HTML version deleted]]

Hi Varpal, What kind of probes are they (what platform)? Have you read the posting guide? A lot of people find it very helpful. http://www.bioconductor.org/docs/postingGuide.html If you are trying to match probes to entrez gene Ids you might want to start by reading the vignettes in AnnotationDbi found here: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.h tml For Arabidopsis, entrez gene Ids can be found in the org.At.tair.db package. And, you can map to them by using the TAIR identifiers presented by the probe package of your choice (from the ACCNUM mapping in the probe package). Please let us know if you need further clarifications. so for example if you had probe ids from the affy "ag" platform: library(ag.db) ids = c("11987_at","11988_at","11989_at") probeTAIR = toTable(agACCNUM[ids]) merge(probeTAIR, toTable(org.At.tairENTREZID)) Marc On 05/11/2010 02:02 AM, Sean Davis wrote: > On Tue, May 11, 2010 at 2:15 AM, varpal singh <gilvarpal at="" gmail.com=""> wrote: > > >> Hi Sir,, >> >> I would like to know about entrez id of arabidopsis, I have probe ids of >> differential expressed genes, I wan to know about their entrez id by >> bioconductor, how van i get?? >> Please tell me!! >> >> >> > Hi, Varpal. > > Please write to the bioconductor email list when asking questions. You will > get better answers there and many people can benefit from those answers. > > As to your question, you'll need to be more specific about what you have > done. In particular, what array are you using? Also, when asking questions > on the list, be sure to include the output of sessionInfo(). > > Sean > > [[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 > >

Dear Madam/SIr, I would like to know how can I get entrez id for arabidopsis, on the basis of probe ids in microarray by bioconductor ?? I have 198 genes after cut-off for P .value 0.05 and logFC value less than -2 and greater than 2.... I used affymetrix data, I got a reply from bioconductor lists in which they suggested me for *org.At.tair.db *and also send me script but that is not working, like > library(ag.db) > id<-c("259879_at") > accs=toTable(agACCNUM[id]) Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "259879_at" not found Error in toTable(agACCNUM[id]) : error in evaluating the argument 'x' in selecting a method for function 'toTable' am not getting my result, please let me know how can I get entrez ids for my 198 genes in arabidopsis.. Thanks &&Regards Varpal [[alternative HTML version deleted]]

On Wed, May 12, 2010 at 2:43 AM, varpal singh <gilvarpal@gmail.com> wrote: > Thanks for your reply !! I have a list of arrays like 259879_at, > 250464_at, 253416_at, > 257506_at, 259790_s_at. These are the 5 arrays of my 198 arrays. > I think you are talking about these array, if you are talking abt other , > please let me know, I would like to tell the name of experiment GSE2133, > first I compared AIR Vs ANOXIA CEL files. > > Please, Varpal, use "Reply to All" when answering email from the list. If you are using GSE2133, that is run on GPL 198, which is called "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array". That is the name of the chip. Go to the bioconductor website and look at the metadata packages available: http://bioconductor.org/packages/2.6/data/annotation/ Find the appropriate annotation package for your array. There is an annotation package that appears to match your chip type: http://bioconductor.org/packages/2.6/data/annotation/html/ath1121501.d b.html Install this package using biocLite(). Then, read the vignette from the AnnotationDbi package that is entitled "AnnotationDbi: How to use the ".db" annotation packages". After reading that, it should be relatively clear how you can accomplish your task given that you are starting with Affy IDs. > I want to get their entrez ids only. > > I have also found a code for entrez ids like > x<-org.At.tairENTREZID > #get the ORF IDs that are mepped to an ENTREZ gene ID# > meped_gene<-mappedkeys(x) > #convert to a list > xx<-as.list(x[meped_gene]) > if(length(xx)>0) { > #get the entrez gene ids for the first five genes > xx[1:5]} > > But I want just 198 entrez ids of genes. In this code I could not > understand how can I introduc > my genes 198 that is problem here.. > > Can you tell me if you have an idea ?? > > Follow the AnnotationDbi vignette with the appropriate annotation package (given above). If you have questions after going through the AnnotationDbi vignette, be sure to provide the code you are using as a reproducible example, any error messages, and the output of sessionInfo() when asking where to go next. Sean > Varpall > > > On Wed, May 12, 2010 at 1:15 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> >> >> On Tue, May 11, 2010 at 10:18 AM, varpal singh <gilvarpal@gmail.com>wrote: >> >>> Dear Madam/SIr, >>> >>> I would like to know how can I get entrez id for arabidopsis, on the >>> basis >>> of probe ids in microarray by bioconductor ?? >>> I have 198 genes after cut-off for P .value 0.05 and logFC value less >>> than >>> -2 and greater than 2.... >>> I used affymetrix data, >>> >>> >> What is the name of the array? That is the important piece that is >> missing here. >> >> Sean >> >> >>> I got a reply from bioconductor lists in which they suggested me for >>> *org.At.tair.db >>> *and also send me script but that is not working, like >>> >>> > library(ag.db) >>> > id<-c("259879_at") >>> > accs=toTable(agACCNUM[id]) >>> Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : >>> value for "259879_at" not found >>> Error in toTable(agACCNUM[id]) : >>> error in evaluating the argument 'x' in selecting a method for function >>> 'toTable' >>> >>> am not getting my result, please let me know how can I get entrez ids for >>> my >>> 198 genes in arabidopsis.. >>> >>> Thanks &&Regards >>> Varpal >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]