[BioC] goseq problem

[Naomi Altman]

After using edgeR to find differentially expressed genes, I tried to 
follow the instructions in goseq to correct for length bias.


  top$table[1:10,1]
  [1] "ENSG00000138131" "ENSG00000204616" "ENSG00000204876" 
"ENSG00000118972" "ENSG00000143546" "ENSG00000163993" 
"ENSG00000012223" "ENSG00000188257"
  [9] "ENSG00000140403" "ENSG00000059804"
geneLengths=getlength(top$table[,1],'hg19','ensGene')
geneLengths[1:10]
  [1] 3672.0 2033.5 2675.5 3021.0  454.0  512.0 1813.0  911.5 2877.0 3504.0

(so far, so good)

pwf=nullp(top$table[,1],'hg19','ensGene')
Loading hg19 length data...
Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed

 > sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United 
States.1252

attached base packages:
[1] tools     grid      stats     graphics  grDevices 
utils     datasets  methods   base

other attached packages:
  [1] goseq_1.2.0            geneLenDataBase_0.99.5 
BiasedUrn_1.03         qvalue_1.24.0          sagenhaft_1.20.0 
SparseM_0.86
  [7] 
edgeR_2.0.5            hexbin_1.24.1          DESeq_1.2.1 
locfit_1.5-6           lattice_0.19-17        akima_0.5-4
[13] Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] annotate_1.28.1      AnnotationDbi_1.12.0 
Biostrings_2.18.4    BSgenome_1.18.3      DBI_0.2-5 
genefilter_1.32.0
  [7] 
geneplotter_1.28.0   GenomicRanges_1.2.3  IRanges_1.8.9 
limma_3.6.9          Matrix_0.999375-46   mgcv_1.7-3
[13] 
nlme_3.1-98          RColorBrewer_1.0-2   RCurl_1.5-0.1 
RSQLite_0.9-4        rtracklayer_1.10.6   splines_2.12.2
[19] 
survival_2.36-5      tcltk_2.12.2         XML_3.2-0.2 
xtable_1.5-6
 >