[BioC] GOSeq error

[Iain Gallagher]

Hello List

I'm using GOSeq to examine the biology behind genes found to be regulated in a RNA-Seq study. One of my comparisons yields ~450 regulated genes. Attempting to run GOSeq with this list results in the following error:

Error in if (min(fv) < lower_bound) fv = fv - min(fv) + lower_bound : 
  missing value where TRUE/FALSE needed


The same script works flawlessly (or at least gives me biologically relevant answers) with other comparisons.

Could anyone shed any light on this error message? Is it simply indicative of a lack of significant enrichment?


Thanks

Iain

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=C                LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] reshape2_1.2.1         annotate_1.32.1        KEGG.db_2.6.1         
 [4] GO.db_2.6.1            goseq_1.6.0            geneLenDataBase_0.99.8
 [7] BiasedUrn_1.04         org.Bt.eg.db_2.6.4     RSQLite_0.11.1        
[10] DBI_0.2-5              AnnotationDbi_1.16.11  Biobase_2.14.0        
[13] edgeR_2.4.3            limma_3.10.2          

loaded via a namespace (and not attached):
 [1] biomaRt_2.10.0        Biostrings_2.22.0     BSgenome_1.22.0      
 [4] GenomicFeatures_1.6.7 GenomicRanges_1.6.6   grid_2.14.1          
 [7] IRanges_1.12.5        lattice_0.20-0        Matrix_1.0-3         
[10] mgcv_1.7-13           nlme_3.1-103          plyr_1.7.1           
[13] RCurl_1.9-5           rtracklayer_1.14.4    stringr_0.6          
[16] tools_2.14.1          XML_3.9-2             xtable_1.6-0         
[19] zlibbioc_1.0.0