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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