topGO desperation
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@oertlin-christian-stud-fhml-5938
Last seen 9.6 years ago
Dear mr/mrs, First of all, I am a new R user. ;) I am currently working with GOdata, and I want to try to map this data visually with R using topGO. My problem begins in the very beginning. I cannot find to load my data into R that it get's recognised as library or anything else I can work with. So my question what do I have to do to load my data (GO file) into topGO. Here is my script so far, not much but a beginning. #set working directory setwd("/Users/christianoertlin/Desktop/Stage files/R") #Use soure bioconductor.org<http: bioconductor.org=""> source("http://bioconductor.org/biocLite.R") #open library library(topGO) library (AnnotationDbi) #load GO file into R here are my troubles Kind regards, Christian Oertlin [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Christian, On 5/13/2013 5:22 AM, Oertlin, Christian (Stud. FHML) wrote: > Dear mr/mrs, > > First of all, I am a new R user. ;) > I am currently working with GOdata, and I want to try to map this data visually with R using topGO. > > My problem begins in the very beginning. I cannot find to load my data into R that it get's recognised as library or anything else I can work with. So my question what do I have to do to load my data (GO file) into topGO. > > Here is my script so far, not much but a beginning. > > #set working directory > setwd("/Users/christianoertlin/Desktop/Stage files/R") > > #Use soure bioconductor.org<http: bioconductor.org=""> > source("http://bioconductor.org/biocLite.R") > #open library > library(topGO) > library (AnnotationDbi) > #load GO file into R here are my troubles As a first step, you should read 'An Introduction to R' (http://cran.r-project.org/doc/manuals/r-release/R-intro.pdf). You will not be able to get very far with BioC if you don't know how to load data into R. Being at least semi-competent with R itself is a crucial aspect to using BioC, so learning the basics is time well spent. Additionally, although you have given some code here, you aren't giving us much to go on. What is your GO file? What is in it? What have you tried to read it into R? Did it fail? If so, what was the error message? Best, Jim > > > Kind regards, > Christian Oertlin > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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@oertlin-christian-stud-fhml-5938
Last seen 9.6 years ago
Hey Jim, well I guess the problem lies somewhere in how the file is built up. But I cannot find how it should be. setwd("/Users/christianoertlin/Desktop/Stage files/R") read.csv("first.csv", header=TRUE, sep=",") library(topGO) read.table("first.csv",header=TRUE,sep=",") resultFisher <- runTest("first.csv", algrotithm="classic",statistic="Fisher") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?runTest? for signature ?"character", "missing", "character"? This is my problem. The fisher test does not recognize my file as something to work with. I tried moving some rows in the file but it did not work either. Tbh I have no clue what is wrong with it. I added the file in the mail. The file is an output generated by GO-elite. I already have my GO term with an outcome I just want to do some test and map them into a graph. Like it is done with the from the topGO example. showSigOfNodes(GOdata, score(resultKS.elim), firstSigNodes = 5, useInfo = 'all') Kind Regards, Christian
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Hi Christian, On 5/16/2013 8:14 AM, Oertlin, Christian (Stud. FHML) wrote: > Hey Jim, > > well I guess the problem lies somewhere in how the file is built up. But I cannot find how it should be. > > setwd("/Users/christianoertlin/Desktop/Stage files/R") > read.csv("first.csv", header=TRUE, sep=",") > library(topGO) > read.table("first.csv",header=TRUE,sep=",") > resultFisher<- runTest("first.csv", algrotithm="classic",statistic="Fisher") > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?runTest? for signature ?"character", "missing", "character"? > > This is my problem. The fisher test does not recognize my file as something to work with. I tried moving some rows in the file but it did not work either. Tbh I have no clue what is wrong with it. I added the file in the mail. > > The file is an output generated by GO-elite. I already have my GO term with an outcome I just want to do some test and map them into a graph. Like it is done with the from the topGO example. Well, I can't help you much because I don't know anything about GO-elite, and the list strips off most attachments (and I wouldn't have opened it anyway. Nothing personal, but I don't even like opening attachments from people I know). A couple of pointers. First, both your read.csv and read.table arguments will just spill the input to your screen rather than saving in an object. If you want the data to persist, you have to assign to an object like thus: dat <- read.csv("first.csv") and note that you don't have to repeat default arguments (header is already TRUE, and sep is already ","). I don't know much about topGO, as I have always preferred to use GOstats (of course I am being a homer, as I contributed to GOstats, but GOstats was written and is maintained by the core group of Bioconductor, so you are more likely to get help for that package on this list). I do know that the first argument to runTest() isn't a file name, but a topGOdata object, so you will have to figure out how to build such a thing first. You might want to look here: http://bioconductor.org/packages/2.12/bioc/vignettes/topGO/inst/doc/to pGO.pdf for help. Or you could take (IMO) the easier route and use GOstats http://bioconductor.org/packages/2.12/bioc/vignettes/GOstats/inst/doc/ GOstatsHyperG.pdf http://bioconductor.org/packages/2.12/bioc/vignettes/GOstats/inst/doc/ GOvis.pdf but you don't say what the array used was, nor the organism. This might make things more difficult. If you are using a less common organism or platform, you might want to look here: http://bioconductor.org/packages/2.12/bioc/vignettes/GOstats/inst/doc/ GOstatsForUnsupportedOrganisms.pdf But you would first do yourself a big favor by reading An Introduction to R http://cran.r-project.org/doc/manuals/r-release/R-intro.pdf so you can better familiarize yourself with R first. Best, Jim > > showSigOfNodes(GOdata, score(resultKS.elim), firstSigNodes = 5, useInfo = 'all') > > Kind Regards, > Christian > > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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