Hi all,

I have solved the problem above by creating a character vector of the list
of genes.

thanks and sorry
Assa


On Thu, Apr 24, 2014 at 10:37 AM, Assa Yeroslaviz <frymor@gmail.com> wrote:

> 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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