Hello,

I am attempting to perform a gene ontology enrichment analysis. I am applying the goana function to my MArrayLM object returned from the eBayes fit. When I use the following code, it returns an error:

eset<-rma(CELdat, background=TRUE, normalize=TRUE, subset=NULL, target="core")     
library(affycoretools)
eset <- annotateEset(eset, annotation(eset))

library(org.Dr.eg.db)
fd <- fData(eset)
fd$ENTREZID <- mapIds(org.Dr.eg.db, as.character(fd$SYMBOL), "ENTREZID","SYMBOL",multiVals="first")
fData(eset) <- fd

library(limma)
design = model.matrix(~ 0 + f)
colnames(design)=c("control","morphant","rescue")
design
data.fit = lmFit(eset,design)
contrast.matrix = makeContrasts(morphant-control,rescue-control,morphant-rescue,levels=design)
data.fit.con = contrasts.fit(data.fit,contrast.matrix)
data.fit.eb = eBayes(data.fit.con)

go <- goana(data.fit.eb, coef=1,geneid=data.fit.eb$genes$ENTREZID,species="dre",convert=TRUE)

Error in goana.default(de = DEGenes, universe = universe, ...) : 
  org.dre.eg.db package required but not not installed (or can't be loaded)

I downloaded the packages (org.Dr.eg.db, pd.zebgene.1.1.st) for the microarray platform (Affy 1.1 ST Zebrafish Gene Array) but it seemingly cant be loaded. Can anyone help me with the GO enrichment here?

Thanks,

Matt

R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] edgeR_3.14.0             limma_3.28.21            org.Dr.eg.db_3.3.0      
 [4] AnnotationDbi_1.34.4     affycoretools_1.44.3     pd.zebgene.1.1.st_3.12.0
 [7] RSQLite_1.0.0            DBI_0.5-1                oligo_1.36.1            
[10] Biostrings_2.40.2        XVector_0.12.1           IRanges_2.6.1           
[13] S4Vectors_0.10.3         Biobase_2.32.0           oligoClasses_1.34.0     
[16] BiocGenerics_0.18.0 

You have typed species="dre" when you meant species="Dr". You have to use exactly the right letters and capitalization.

There is no argument 'convert' for goana() and no need to convert IDs anyway. Please read the help page. I think you may be getting confused with kegga(). The two functions have slightly different arguments because goana() uses annotation information stored in Bioconductor annotation packages whereas kegga() uses annotation read from the KEGG webpage. For example, you have to use Bioconductor-style species names for goana() instead of KEGG-style names.

Also, did you know that you can just use geneid="ENTREZID"? You don't have to specify the whole object path.