[BioC] ChIPpeakAnno::getEnrichedGo crashes but I don't know why

[Eric Cabot]

I am a relatively new Bioconductor user and I am trying to analyze some 
ChIP-seq results that came from QuEST using the ChIPpeakAnno package.

After importing the regions of interest into RangedData objects and doing 
the following:

ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, 
featureType="ExonPlusUtr")


I had no problem annotating  and generating  a Venn diagram to show the 
overlaps between my three sets of peaks. To annotate, I used:

annotated_regions=annotatePeakInBatch(myranged, 
AnnotationData=ENSEMBL_ExonPlus_Annotation)


But I cannot seem to get the getEnrichedGo method to work on this (or my 
other two annotated regions). Here is a typical command line:


my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.01,multiAdj=TRUE,minGOterm=1,
multiAdjMethod="BH",feature_id_type="ensembl_gene_id")

and here is a typical error message:

enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.01,multiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id")
Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
   argument is of length zero


Which leads me to ask:

1) Is this error message supposed to be meaningful to me-i.e. a user-or is 
it something that I should be sending to the developer of the package?

2) Is there anything obvious from this that suggests what corrective 
action I should be taking?


Eric Cabot
University of Wisconsin