[BioC] hyperGTest Error in sqliteExecStatement...

[Robert Gentleman]

Hi Christopher,
    Thanks for the report.  Part of the reason to ask for a 
self-contained example is that there is some chance that you have 
personally actually run it, and part of the reason is to make it easy 
for me (or someone who might want to help) to cut and paste from your 
email.  Your example fails on both counts.  I have to edit out the > and 
other bits that you cut from your R session before I can run it, and 
this script doesn't run, as all calls to library are missing

Adding these to the start:

  library(ALL)
   library(hgu95av2.db)
   library(genefilter)
   library(GOstats)

yields something that runs just fine in the current release, so I can 
only suggest that you update your R, and bioc appropriately and you 
should have no problems.

   Part of your problem may also stem from the fact that you are doing 
exactly what we advise against, and that is mixing and matching 
different versions of packages inappropriately.  Please use biocLite - 
it is intended to keep you from having these sorts of problems.

  best wishes
    Robert


other attached packages:
  [1] GOstats_2.6.0       Category_2.6.0      RBGL_1.16.0
  [4] annotate_1.18.0     xtable_1.5-2        GO.db_2.2.0
  [7] graph_1.18.0        genefilter_1.20.0   survival_2.34-1
[10] hgu95av2.db_2.2.0   AnnotationDbi_1.2.0 RSQLite_0.6-8
[13] DBI_0.2-4           ALL_1.4.3           Biobase_2.0.0



Christopher Brown wrote:
> Bioconductors-
> I have produced the following error upon calling hyperGTest with  
> several different datasets.  I have reproduced the error below using  
> data from the ALL set and code parsed from the GOStats vignette.  Any  
> help would be appreciated.  Cheers,
> 
> -Casey
> 
>  > data(ALL, package = "ALL")
>  > Bcell <- grep("^B", as.character(ALL$BT))
>  > subsetType <- "ALL/AF4"
>  > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG",  
> subsetType))
>  > bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)]
>  > bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol)
>  >
>  > entrezIds <- mget(featureNames(bcrAblOrNeg), envir =  
> hgu95av2ENTREZID)
>  > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) ! 
> is.na(x))]
>  > bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ]
>  > haveGo <- sapply(mget(featureNames(bcrAblOrNeg), hgu95av2GO),
> + function(x) { if (length(x) == 1 && is.na(x)) FALSE else TRUE })
>  > bcrAblOrNeg <- bcrAblOrNeg[haveGo, ]
>  >
>  > iqrCutoff <- 0.5
>  > bcrAblOrNegIqr <- apply(exprs(bcrAblOrNeg), 1, IQR)
>  > selected <- bcrAblOrNegIqr > iqrCutoff
>  >
>  > nsFiltered <- bcrAblOrNeg[selected, ]
>  > nsFilteredIqr <- bcrAblOrNegIqr[selected]
>  > uniqGenes <- findLargest(featureNames(nsFiltered), nsFilteredIqr,
> + "hgu95av2")
>  > nsFiltered <- nsFiltered[uniqGenes, ]
>  >
>  > ttestCutoff <- 0.05
>  > ttests = rowttests(nsFiltered, "mol.biol")
>  > smPV = ttests$p.value < ttestCutoff
>  > pvalFiltered <- nsFiltered[smPV, ]
>  > selectedEntrezIds <- unlist(mget(featureNames(pvalFiltered),
> + hgu95av2ENTREZID))
>  >
>  > hgCutoff <- 0.001
>  > params <- new("GOHyperGParams", geneIds = selectedEntrezIds,  
> annotation = "hgu95av2.db",
> + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,
> + testDirection = "over")
>  >
>  > hgOver <- hyperGTest(params)
> Error in sqliteExecStatement(con, statement, bind.data) :
>    RS-DBI driver: (error in statement: cannot join using column _id -  
> column not present in both tables)
> 
>  > traceback()
> 13: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE  
> = .SQLitePkgName)
> 12: sqliteExecStatement(con, statement, bind.data)
> 11: sqliteQuickSQL(conn, statement, ...)
> 10: dbGetQuery(db, SQL)
> 9: dbGetQuery(db, SQL)
> 8: getGoToEntrezMap_db(p)
> 7: categoryToEntrezBuilder(p)
> 6: categoryToEntrezBuilder(p)
> 5: .class1(object)
> 4: .class1(object)
> 3: is(object, Cl)
> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase",
>         "hyperGTest")
> 1: hyperGTest(params)
> 
>  > sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-apple-darwin8.10.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets  methods   base
> 
> other attached packages:
>   [1] RColorBrewer_1.0-2  GOstats_2.4.0       Category_2.6.0       
> RBGL_1.14.0         graph_1.18.0
>   [6] genefilter_1.16.0   survival_2.34       annotate_1.16.1      
> xtable_1.5-2        GO.db_2.0.2
> [11] hgu95av2.db_2.0.2   AnnotationDbi_1.0.6 RSQLite_0.6-8        
> DBI_0.2-4           ALL_1.4.3
> [16] Biobase_1.16.3
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.9
> 
> 
> 
> 
> 
> ------------------------
> Christopher Brown
> Institute for Genomics and Systems Biology
> University of Chicago
> CLSC Room 431
> 920 E. 58th. St.
> Chicago, IL, 60637
> Lab: (773) 834-0074
> caseybrown [at] uchicago.edu
> 
> 
> 
> 
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org