Hi Josh and Bioc User,

I am having a problem creating the GO HTML report for a gene set out of
GOstats analysis.

Here is what I do:

selectedIDs <- resSig$entrez
#selectedIDs <- na.omit(selectedIDs) # not sure if needed
universeIDs <- res$entrez
# universeIDs <- na.omit(universeIDs) # not sure if needed
goParams <- new("GOHyperGParams",
    geneIds = selectedIDs,
    universeGeneIds = universeIDs,
    annotation ="org.Mm.eg" ,
    ontology = "BP",
    pvalueCutoff = 0.01,
    conditional = TRUE,
    testDirection = "over")
goResults <- hyperGTest(goParams)
df <- summary(goResults)
#dim(summary(goResults, pvalue=0.1))
#dim(summary(goResults, categorySize=10))
htmlReport(goResults, file="test_report.html") # this works just fine

BPReport <- HTMLReport(shortName ='GO-BP_analysis_rnaseq', title =
paste("GO analysis of DE genes in the comparisonn of ", group1, "vs.",
group2, sep="") ,reportDirectory = "./GO_reports")
publish(goResults, BPReport, selectedIDs=selectedIDs, annotation.db="
org.Mm.eg",pvalueCutoff= 0.05, makePlot=TRUE)
finish(BPReport)

But when I run the publidh command I get the error:

Error in unlist(mget(ids, ann.map, ifnotfound = NA)) :
  error in evaluating the argument 'x' in selecting a method for function
'unlist': Error in .checkKeysAreWellFormed(keys) :
  keys must be supplied in a character vector with no NAs


I also tried your example from the web site (
http://research-pub.gene.com/ReportingTools/microarray3.R) and got a
similar error massage:

library(GOstats)
tt <- topTable(fit, coef = 2, n = 100)
selectedIDs <- unlist(mget(tt$ID, hgu95av2ENTREZID))
universeIDs <- unlist(mget(featureNames(ALL), hgu95av2ENTREZID))
goParams <- new("GOHyperGParams",
     geneIds = selectedIDs,
    universeGeneIds = universeIDs,
     annotation = annotation(ALL),
     ontology = "BP",
    pvalueCutoff = 0.01,
     conditional = TRUE,
     testDirection = "over")
 goResults <- hyperGTest(goParams)


###################################################
### Make the GO report
###################################################
goReport <- HTMLReport(shortName = 'go_analysis',
                       title = 'GO analysis of BCR/ABL translocation',
                       reportDirectory = './reports')
publish(goResults, goReport, selectedIDs = selectedIDs, annotation.db
= 'org.Hs.eg')


Warning message:
No results met the specified criteria.  Returning 0-row data.frame

Error in unlist(mget(ids, ann.map, ifnotfound = NA)) :
  error in evaluating the argument 'x' in selecting a method for
function 'unlist': Error in .checkKeysAreWellFormed(keys) :
  keys must be supplied in a character vector with no NAs

So I guess the prolem is not with my data set.
I would like to know if this have anything to do with the new version of R?

thanks in afdvance,

Assa


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] xtable_1.7-3            org.Mm.eg.db_2.14.0     GOstats_2.30.0
 [4] graph_1.42.0            Category_2.30.0         GO.db_2.14.0
 [7] Matrix_1.1-2            biomaRt_2.20.0          edgeR_3.6.0
[10] limma_3.20.1            ReportingTools_2.4.0    AnnotationDbi_1.26.0
[13] Biobase_2.24.0          RSQLite_0.11.4          DBI_0.2-7
[16] knitr_1.5               rtracklayer_1.24.0      gplots_2.13.0
[19] RColorBrewer_1.0-5      genefilter_1.46.0       DESeq2_1.4.0
[22] RcppArmadillo_0.4.200.0 Rcpp_0.11.1             GenomicRanges_1.16.2
[25] GenomeInfoDb_1.0.2      IRanges_1.22.3          BiocGenerics_0.10.0
[28] BiocInstaller_1.14.1

loaded via a namespace (and not attached):
 [1] annotate_1.42.0          AnnotationForge_1.6.0
BatchJobs_1.2
 [4] BBmisc_1.5               BiocParallel_0.6.0
Biostrings_2.32.0
 [7] biovizBase_1.12.0        bitops_1.0-6
brew_1.0-6
[10] BSgenome_1.32.0          caTools_1.17
cluster_1.14.4
[13] codetools_0.2-8          colorspace_1.2-4
dichromat_2.0-0
[16] digest_0.6.4             evaluate_0.5.3
fail_1.2
[19] foreach_1.4.2            formatR_0.10
Formula_1.1-1
[22] gdata_2.13.3             geneplotter_1.42.0
GenomicAlignments_1.0.0
[25] GenomicFeatures_1.16.0   ggbio_1.12.0
ggplot2_0.9.3.1
[28] grid_3.1.0               gridExtra_0.9.1
GSEABase_1.26.0
[31] gtable_0.1.2             gtools_3.4.0
Hmisc_3.14-4
[34] hwriter_1.3              iterators_1.0.7
KernSmooth_2.23-10
[37] lattice_0.20-24          latticeExtra_0.6-26
locfit_1.5-9.1
[40] MASS_7.3-29              munsell_0.4.2
PFAM.db_2.14.0
[43] plyr_1.8.1               proto_0.3-10
RBGL_1.40.0
[46] RCurl_1.95-4.1           reshape2_1.2.2
R.methodsS3_1.6.1
[49] R.oo_1.18.0              Rsamtools_1.16.0
R.utils_1.29.8
[52] scales_0.2.4             sendmailR_1.1-2
splines_3.1.0
[55] stats4_3.1.0             stringr_0.6.2
survival_2.37-7
[58] tools_3.1.0              VariantAnnotation_1.10.0
XML_3.98-1.1
[61] XVector_0.4.0            zlibbioc_1.10.0

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