Hi

I was doing a gene ontology analysis on a set of differentially expressed genes. The goana function returns an error saying ," No genes found in universe". Here is the code I ran for differential expression analysis ('countdata' represents the dataframe containing counts of each gene in each of the samples) :

> gns <- select(org.Hs.eg.db, row.names(countdata), c("ENTREZID","SYMBOL"),"ENSEMBL")
'select()' returned 1:many mapping between keys and columns
> gns <- gns[!duplicated(gns[,1]),]
> all.equal(gns$ENSEMBL, row.names(countdata))
[1] TRUE

>condition <- c(rep("Control",3),rep("Resistant",2))

y <- DGEList(countdata, genes = gns,group=condition)
> countsPerMillion <- cpm(y)
> keep <- which(rowSums(countCheck) >= 2)
> y <- y[keep,]
> y <- calcNormFactors(y, method="TMM")
> plotMDS(y)
> design=model.matrix(~condition,y$samples)

> y <- estimateDisp(y,design)
> plotBCV(y)
> fit <- glmFit(y,design)
> lrt <- glmLRT(fit,coef=2)
> edgeR_result = topTags(lrt, n=24000, adjust.method="BH", sort.by="PValue", p.value=0.05)

> deGenes=decideTestsDGE(lrt, adjust.method="BH", p.value=0.05, lfc=1)
> summary(deGenes)
   [,1] 
-1   353
0  13399
1    348
> deGenes=row.names(lrt)[as.logical(deGenes)]
> plotSmear(lrt,de.tags=deGenes)
> go <- goana(lrt)
Error in goana.default(de = DEGenes, universe = universe, ...) : 
  No genes found in universe.

> traceback()
5: stop("No genes found in universe")
4: goana.default(de = DEGenes, universe = universe, ...)
3: goana(de = DEGenes, universe = universe, ...)
2: goana.DGELRT(lrt)
1: goana(lrt)

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7600)

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

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

other attached packages:
 [1] org.Hs.eg.db_3.4.0   AnnotationDbi_1.36.2 Biobase_2.34.0      
 [4] BiocInstaller_1.24.0 edgeR_3.16.5         limma_3.30.13       
 [7] rtracklayer_1.34.2   GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 
[10] IRanges_2.8.2        S4Vectors_0.12.2     fastcluster_1.1.24  
[13] reshape2_1.4.2       ggplot2_2.2.1        RSQLite_2.0         
[16] BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] bitops_1.0-6               matrixStats_0.52.2         bit64_0.9-7               
 [4] RColorBrewer_1.1-2         httr_1.3.1                 tools_3.3.2               
 [7] R6_2.2.2                   DBI_0.7                    lazyeval_0.2.0            
[10] colorspace_1.3-2           bit_1.1-12                 cummeRbund_2.16.0         
[13] scales_0.5.0               stringr_1.2.0              digest_0.6.12             
[16] Rsamtools_1.26.2           XVector_0.14.1             pkgconfig_2.0.1           
[19] htmltools_0.3.6            BSgenome_1.42.0            rlang_0.1.2               
[22] BiocParallel_1.8.2         VariantAnnotation_1.20.3   RCurl_1.95-4.8            
[25] magrittr_1.5               GO.db_3.4.0                Matrix_1.2-11             
[28] Rcpp_0.12.13               munsell_0.4.3              stringi_1.1.5             
[31] SummarizedExperiment_1.4.0 zlibbioc_1.20.0            plyr_1.8.4                
[34] blob_1.1.0                 lattice_0.20-35            Biostrings_2.42.1         
[37] splines_3.3.2              GenomicFeatures_1.26.4     locfit_1.5-9.1            
[40] biomaRt_2.30.0             XML_3.98-1.9               latticeExtra_0.6-28       
[43] data.table_1.10.4          gtable_0.2.0               tibble_1.3.4              
[46] GenomicAlignments_1.10.1   memoise_1.1.0             

Kindly support.

I was able to solve it by giving the column name of ENTREZID  for "geneid " in goana function.