Dear Matthew,
I am getting the following error when using goseq. Any idea what may cause it?
Thanks,
Adi

> pwf=nullp(genes,bias.data=cntbias)
> gocats=as.list(org.Hs.egGO2ALLEGS)
> GOr=goseq(pwf,gene2cat=gocats)
Using manually entered categories.
Calculating the p-values...
Error in dWNCHypergeo(num_de_incat, num_incat, num_genes - num_incat,  :
  Negative parameter
> head(pwf)
          DEgenes bias.data        pwf
642819          0      3764 0.05775376
414235          0       124 0.02107342
57107           0     14702 0.06023892
649159          1       248 0.02542837
3127            0     44633 0.06357525
100507412       1      1337 0.05268580
> head(gocats[3:5])
$`GO:0000012`
        IDA         IDA         IEA         IMP         IDA         IDA
     "3981"      "7141"      "7515"     "23411"     "54840"     "55775"
        IMP         IMP         IEA
    "55775"    "200558" "100133315"

$`GO:0000018`
     IEA      IEA      IMP      IEA      IEA      IDA      IDA      IEA
   "604"    "641"    "641"    "940"    "958"   "1111"   "2956"   "3458"
     IEA      ISS      TAS      TAS      NAS      TAS      TAS      IEA
  "3558"   "3565"   "3565"   "3575"   "3586"   "3836"   "3838"   "4292"
     TAS      IBA      IDA      ISS      IDA      IMP      IMP      IEA
  "4361"   "4436"   "4436"   "4436"   "4437"   "5531"   "6118"   "6778"
     IDA      IEA      IDA      IEA      IDA      IEA      ISS      ISS
  "7040"   "7320"   "8741"   "9466"  "10111"  "11105"  "22976"  "23529"
     IEA      IBA      IDA      IMP      ISS      IMP      IEA      IEA
 "30009"  "50943"  "51548"  "51750"  "54386"  "55010"  "56154"  "56852"
     IEP      IMP      IEA      IMP
 "56916"  "56979"  "80762" "151987"

$`GO:0000019`
    IEA     IEA     TAS     IDA
  "641"  "4292"  "4361" "10111"

> sessionInfo()
R version 2.15.3 RC (2013-02-24 r62054)
Platform: x86_64-unknown-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=C                 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] KEGG.db_2.8.0           goseq_1.10.0            geneLenDataBase_0.99.10
[4] BiasedUrn_1.05          GO.db_2.8.0             GOstats_2.24.0
 [7] graph_1.36.2            Category_2.24.0         org.Hs.eg.db_2.8.0
[10] RSQLite_0.11.2          DBI_0.2-5               BiocInstaller_1.8.3
[13] edgeR_3.0.8             limma_3.14.4            rtracklayer_1.18.2
[16] multicore_0.1-7         Rsamtools_1.10.2        Biostrings_2.26.3
[19] GenomicFeatures_1.11.13 AnnotationDbi_1.20.6    Biobase_2.18.0
[22] GenomicRanges_1.11.31   IRanges_1.17.35         BiocGenerics_0.5.6

loaded via a namespace (and not attached):
[1] annotate_1.36.0       AnnotationForge_1.0.3 biomaRt_2.14.0
 [4] bitops_1.0-5          BSgenome_1.26.1       genefilter_1.40.0
 [7] grid_2.15.3           GSEABase_1.20.2       lattice_0.20-13
[10] Matrix_1.0-11         mgcv_1.7-22           nlme_3.1-108
[13] RBGL_1.34.0           RCurl_1.95-4.1        splines_2.15.3
[16] stats4_2.15.3         survival_2.37-4       tools_2.15.3
[19] XML_3.95-0.2          xtable_1.7-1          zlibbioc_1.4.0



Adi Laurentiu TARCA, Ph.D.
Assistant Professor (Research),
Department of Computer Science & Center for Molecular Medicine and Genetics, Wayne State University,
Director, Bioinformatics and Computational Biology Unit,  Perinatology Research Branch (NICHD),
3990 John R., Office 4809,
Detroit, Michigan 48201
Tel: 1-313-5775305


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