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

[Zhu, Lihua (Julie)]

Hi Eric,

Could you please post the session information with sessionInfo() command?
Could you please also send a few ensembl IDs in your annotated dataset?
Thanks!

Best regards,

Julie


On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at gmail.com> wrote:

> 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,mu
> ltiAdj=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
> 
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