James, Thanks ever so much. Following your advice, I was able to get this to work quite nicely. Regards, Maureen On 2/15/11 9:51 AM, James W. MacDonald wrote: > Hi Maureen, > > On 2/14/2011 5:50 PM, Maureen J. Donlin wrote: >> James, >> >> Thanks for the reply. I figured out how to get the data into a data >> frame. >> I was doing 2 things wrong, but here is the code that worked. >> >> > CneoGO <- read.table("Cneo_GOannot.txt", header=TRUE) >> > head(CneoGO) >> Goterm Evidence GeneID >> 1 GO:0015893 IEA CNAG_00003 >> 2 GO:0043231 IEA CNAG_00003 >> 3 GO:0015203 IEA CNAG_00003 >> 4 GO:0044425 IEA CNAG_00003 >> 5 GO:0044444 IEA CNAG_00003 >> 6 GO:0015846 IEA CNAG_00003 >> >> > goframeData = data.frame(CneoGO$Goterm, CneoGO$Evidence, >> CneoGO$GeneID) >> > head(goframeData) >> CneoGO.Goterm CneoGO.Evidence CneoGO.GeneID >> 1 GO:0015893 IEA CNAG_00003 >> 2 GO:0043231 IEA CNAG_00003 >> 3 GO:0015203 IEA CNAG_00003 >> 4 GO:0044425 IEA CNAG_00003 >> 5 GO:0044444 IEA CNAG_00003 >> 6 GO:0015846 IEA CNAG_00003 > > This step is unnecessary. The result of read.table() *is* a > data.frame, so you are just creating another data.frame here. > >> >> So continuing with the tutorial guide, I executed the following: >> >> > library("GSEABase") >> Loading required package: annotate >> >> > goFrame = GOFrame(goframeData, organism = "Cryptococcus neoformans") >> Loading required package: GO.db >> >> > goFrame >> An object of class "GOFrame" >> Slot "data": >> CneoGO.Goterm CneoGO.Evidence CneoGO.GeneID >> 1 GO:0015893 IEA CNAG_00003 >> 2 GO:0043231 IEA CNAG_00003 >> ... >> Slot "organism": >> [1] "Cryptococcus neoformans" >> >> > goAllFrame = GOAllFrame(goFrame) >> >> > goAllFrame >> An object of class "GOAllFrame" >> Slot "data": >> go_id evidence gene_id >> 1 GO:0000001 IEA CNAG_00006 >> 2 GO:0000001 IEA CNAG_00088 >> ... >> Slot "organism": >> [1] "Cryptococcus neoformans" >> >> >> > gsc <- GeneSetCollection(goAllFrame, setType = GOCollection()) >> > gsc >> GeneSetCollection >> names: GO:0000001, GO:0000002, ..., GO:2000045 (6658 total) >> unique identifiers: CNAG_00006, CNAG_00088, ..., CNAG_06995 (4822 total) >> types in collection: >> geneIdType: GOAllFrameIdentifier (1 total) >> collectionType: GOCollection (1 total) >> >> > universe = Lkeys(CneoGO) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "Lkeys", for signature >> "data.frame" > > So here you are getting mixed up with what Marc had to do to get his > example to run, and what you need to do. The 'universe' is just the > complete set of gene IDs from which your significant set was chosen. > > If you had an org.Cn.eg.db package, then you would do something > similar. However, you don't, which is the point of this exercise. The > corresponding set of gene IDs that you do have is the third column of > the data.frame you created above (goFrameData or CneoGO). > > Note here that you want to make sure that the gene IDs you use are > character values, not factors. The default for R when reading in a > data.frame is to convert a vector of strings to factor, so you either > want to use > > CneoGO <- read.table("Cneo_GOannot.txt", header=TRUE, stringsAsFactors > = FALSE) > > and then > > universe <- CneoGO[,3] > > or proceed as you already have, but then > > universe <- as.character(CneoGO[,3]) > > In addition, note that you will need to construct your 'genes' vector > differently from what is shown on p.3 of the vignette, instead > selecting the set of significant genes from the results of your > analysis (again, using the CNAG gene IDs). > > From that point on, you continue as Marc shows in the vignette. > > Best, > > Jim > > > >> >> Am I missing some data that is found in the library("org.Hs.egGO")? I >> can do the same commands with it and the structure of the goFrame, >> goAllFrame and gsc seem to be the same. >> >> Here's what I am trying to do. I have a microarray data set from a time >> course experiment done with a fungal genome, C. neoformans. I have >> clusters of genes which are associated based how their expression >> changed in relation to the other genes on the array. So what I have are >> gene lists, with no expression data or fold changes. For each list of >> genes, I want to know what GO terms are over-represented. >> >> I apologize if these questions are too basic. It's just that most of the >> software out there for gene enrichment analysis are designed for model >> organisms. >> >> Again, any help is greatly appreciated. >> >> Regards, >> Maureen >> >> >> >> >> >> On 2/14/11 3:23 PM, James W. MacDonald wrote: >>> Hi Maureen, >>> >>> On 2/14/2011 3:27 PM, Maureen J. Donlin wrote: >>>> Hi all, >>>> >>>> I'm new to R and have some very basic questions about using GOstats >>>> with >>>> a non-model organism. >>>> I'm trying to use the tutorial by Marc Carlson "How to Use GOstats >>>> and...with unsupported model organisms." >>>> >>>> I've created a GO to gene mapping file with the following 3 columns of >>>> data: >>>> Goterm Evidence GeneID >>>> GO:0015893 IEA CNAG_00003 >>>> GO:0043231 IEA CNAG_00003 >>>> GO:0015203 IEA CNAG_00003 >>>> GO:0044425 IEA CNAG_00003 >>>> ... >>>> >>>> I can import it using read.table, but I don't seem to be able to >>>> invoke >>>> the data frame correctly. >>> >>> When you read it in using read.table(), you automatically have a >>> data.frame. >>> >>>> >>>> The tutorial reads: >>>> library("org.Hs.eg.db") >>>> frame = toTable(org.Hs.egGO) >>>> goFrameData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) >>> >>> Yep, this is just some code that Marc uses to create a data.frame so >>> he can give an example. >>> >>>> >>>> I imported the data into an object using read.table >>>> >CneoGOanno <- read.table("Cneo_GOannot.txt") >>>> >>>> I tried to create a frame using: >>>> > frame = toTable(CneoGOannot) >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function "toTable", for >>>> signature >>>> "data.frame" >>>> >>>> Do I have to create some sort of database for this organism first? If >>>> so, what is it's format? >>>> >>>> Any suggestions would be most appreciated. >>> >>> Just go to the next step, which will be something like >>> >>> goFrame <- GOFrame(CneoGOanno, organism = "Cryptococcus neoformans") >>> goAllFrame <- GOALLFrame(goFrame) >>> >>> >>> Best, >>> >>> Jim >>> >>> >>> >>>> >>>> Regards, >>>> Maureen Donlin >>>> >>>> At the risk of too long of an email, here's the session info: >>>> > sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] org.Hs.eg.db_2.4.6 GOstats_2.16.0 RSQLite_0.9-4 DBI_0.2-5 >>>> graph_1.28.0 Category_2.16.0 AnnotationDbi_1.12.0 >>>> [8] Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.28.0 genefilter_1.32.0 GO.db_2.4.5 GSEABase_1.12.2 >>>> RBGL_1.26.0 splines_2.12.1 survival_2.36-2 tools_2.12.1 >>>> [9] XML_3.2-0 xtable_1.5-6 >>>> >>>> >>> >> > -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Molecular Microbiology& Immunology Dept. of Biochemistry& Molecular Biology Saint Louis University School of Medicine 507 Doisy Research Center 1100 S. Grand St. Louis, MO 63104 Phone: 314-977-8858