Marc, I have attempted to modify my code without success. The reason I was requesting a patch is because I believe the problem is originating within the summary function. Below is my code that generatesa GOHyperGParams object, applies hyperGTest, and then tries to summarize the result. I took a look at the test.object created by hyperGTest to see if it contained GO:ID's that I could remove or subset out as you suggest but it does not contain any. These seem to be fetched my mget called from within summary. I looked at the source code for summary and tried to modify it by having mget return NA ifnotfound (see further below) but this results in a problem with lapply when "standardGeneric for "Term" defined from package "AnnotationDbi"" is the FUN applied to NA. So I am stuck and would appreciate your help. Please see my comment in the R code for where I think a fix should be applied. I understand that this may only occur occasionally and only in BioC-devel, but it would seem useful to those of us who do test BioC- devel. Thanks, Mark ############################################################# #MY CODE params <- new("GOHyperGParams", geneIds = selectedEntrezIds, universeGeneIds = entrez.universe.vec, annotation = annotationPckg, ontology = "BP", pvalueCutoff = minP, conditional = TRUE, testDirection = testDirection) test.obj<-hyperGTest(params) #this is where the blow-up occurs output.table<-data.frame(summary(test.obj)) ###################################################################### # GOstats code from hyperGtable.R ################################################################## setMethod("summary", signature(object="GOHyperGResult"), function(object, pvalue=pvalueCutoff(object), categorySize=NULL, htmlLinks=FALSE) { AMIGO_URL <- "http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_co nstraint=terms&depth=0&query=%s" df <- callNextMethod(object=object, pvalue=pvalue, categorySize=categorySize) if (nrow(df) == 0) { df$Term <- character(0) return(df) } #This is where it would be nice to filter out invalid goIds but I can't # figure out how to do it goIds <- df[[1]] goTerms <- sapply(mget(goIds, GOenv("TERM"), ifnotfound = NA), Term) if (htmlLinks) { goIdUrls <- sapply(goIds, function(x) sprintf(AMIGO_URL, x)) goTerms <- paste('', goTerms, '', sep="") } df$Term <- goTerms df }) Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel<at>gmail<dot>com ****************************************************************** Marc Carlson wrote: > Marc Carlson wrote: >> Mark W Kimpel wrote: >> >>> I have used a custom wrapper function to invoke GOstats for almost a >>> year without problem. Now, with just one dataset, I am getting an error. >>> Not sure if this is a bug or something very odd about just my one >>> dataset. The GO:ID that yields the error is a valid ID, I checked. I am >>> using the devel version and rechecked after just updating my packages. >>> >>> Any ideas as to what the problem might be? >>> >>> Loading required package: rat2302 >>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : >>> invalid key "GO:0016089" >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, >>> custom.contra >>> 2: GO.anal.func(input.df = t.tab.annot.obj$sig.named.genes, >>> annotationPckg = a >>> 3: GOHyperMaxCats.func(optimizedParam) >>> 4: data.frame(summary(test.obj)) >>> 5: summary(test.obj) >>> 6: summary(test.obj) >>> 7: .local(object, ...) >>> 8: sapply(mget(goIds, GOenv("TERM")), Term) >>> 9: lapply(X, FUN, ...) >>> 10: is.vector(X) >>> 11: mget(goIds, GOenv("TERM")) >>> 12: mget(goIds, GOenv("TERM")) >>> 13: `keys<-`(`*tmp*`, value = c("GO:0007268", "GO:0007214", >>> "GO:0050877", "GO:0 >>> 14: `keys<-`(`*tmp*`, value = c("GO:0007268", "GO:0007214", >>> "GO:0050877", "GO:0 >>> 15: switch(as.character(direction(x)), "1" = `Lkeys<-`(x, value), "-1" = >>> `Rkeys >>> 16: `Lkeys<-`(x, value) >>> 17: `Lkeys<-`(x, value) >>> 18: .checkKeys(value, Lkeys(x), x at ifnotfound) >>> >>> >>> > sessionInfo() >>> R version 2.7.0 Under development (unstable) (2007-12-20 r43739) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] rat2302_2.0.1 affycoretools_1.11.2 annaffy_1.11.1 >>> [4] KEGG_2.0.1 GO_2.0.1 gcrma_2.11.1 >>> [7] matchprobes_1.11.0 biomaRt_1.13.6 RCurl_0.8-3 >>> [10] GOstats_2.5.0 Category_2.5.0 genefilter_1.17.7 >>> [13] survival_2.34 RBGL_1.15.7 annotate_1.17.3 >>> [16] xtable_1.5-2 GO.db_2.1.1 AnnotationDbi_1.1.8 >>> [19] RSQLite_0.6-4 DBI_0.2-4 graph_1.17.14 >>> [22] limma_2.13.3 affy_1.17.3 preprocessCore_1.1.5 >>> [25] affyio_1.7.9 Biobase_1.17.8 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.9 XML_1.93-2 >>> >>> > > If you could show me what it is that your script is doing (some source > code) then I might be better able to help you with this. But as it > stands right now I have very few specifics about what you are trying to > do. I can see you posted the sessionInfo() which helps me know what > versions of things you are using. But what is this script that you > speak of? What does that code actually look like? I am afraid that I > don't have a patch for you because the annotation package is not > actually broken, and is only missing information because of what was > available at GO at the precise moment when that package was made. I > can't tell you why GO decided to remove that particular term and then > later on decided to add it back in, but I looked at data that we > gathered from them to build annotations at different time points and > that is what has actually happened in this case. > >>From your previous posts, it looks like your trouble is caused because > you are missing a key and then looking for that missing key in an > environment. If that is what is happening, then I think you should code > things in a way so that you can filter out keys that are not present. > > More specifically I think that you probably just want to do some minor > cleanup before you call something like mget() to make sure that your > keys are actually present. Here is a quick example of how this might look: > > library(GO.db) > > myKeys = c("FAKEID","GO:0000006","GO:0000003") > > myKeys[myKeys %in% keys(GOTERM)] > > > Hope this helps, > > > Marc > > >