Question: TopGO Drosophila ananassae
0
gravatar for koeniger
3.2 years ago by
koeniger10
koeniger10 wrote:

Dear all,

I am trying to do a GO-term enrichment analysis in Drosophila ananassae with TopGO. I used the following code:

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] MeSH.Dan.eg.db_1.6.0       MeSHDbi_1.8.0              BiocInstaller_1.22.3       topGO_2.24.0              
 [5] SparseM_1.7                GO.db_3.3.0                AnnotationDbi_1.34.3       graph_1.50.0              
 [9] RColorBrewer_1.1-2         ggplot2_2.1.0              DESeq2_1.12.3              SummarizedExperiment_1.2.3
[13] Biobase_2.32.0             GenomicRanges_1.24.2       GenomeInfoDb_1.8.1         IRanges_2.6.1             
[17] S4Vectors_0.10.1           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5         plyr_1.8.4          XVector_0.12.0      tools_3.3.0         zlibbioc_1.18.0     digest_0.6.9       
 [7] rpart_4.1-10        RSQLite_1.0.0       annotate_1.50.0     gtable_0.2.0        lattice_0.20-33     Matrix_1.2-6       
[13] DBI_0.4-1           gridExtra_2.2.1     genefilter_1.54.2   cluster_2.0.4       locfit_1.5-9.1      grid_3.3.0         
[19] nnet_7.3-12         data.table_1.9.6    XML_3.98-1.4        survival_2.39-5     BiocParallel_1.6.2  foreign_0.8-66     
[25] latticeExtra_0.6-28 Formula_1.2-1       geneplotter_1.50.0  matrixStats_0.50.2  Hmisc_3.17-4        scales_0.4.0       
[31] splines_3.3.0       colorspace_1.2-6    xtable_1.8-2        labeling_0.3        acepack_1.3-3.3     munsell_0.4.3      
[37] chron_2.3-47   

 

 

mytopgoobject <- new("topGOdata",
                  description = "Slow15down",
                  ontology = "BP",
                  allGenes=Slow15downList,
                  geneSel=topDiffGenes,
                  annot=annFUN.org,
                  nodeSize=5,
                  mapping= "MeSH.Dan.eg.db")

and I get the following error message:

Building most specific GOs .....
Error in get(paste(mapping, "dbconn", sep = "_")) : 
  object 'MeSH.Dan.eg_dbconn' not found

 

To me it seems like the annotation file for D. ananassae is not recognized. Can somebody help me and tell what I am doing wrong?

Thank you!!!!!!!!!!!!!!1

 

 

ADD COMMENTlink modified 3.2 years ago by James W. MacDonald51k • written 3.2 years ago by koeniger10
Answer: TopGO Drosophila ananassae
0
gravatar for James W. MacDonald
3.2 years ago by
United States
James W. MacDonald51k wrote:

Most of the AnnotationDbi objects have a function that allows you to query the underlying database directly. As an example, the org.Hs.eg.db package has a function org.Hs.eg_dbconn, that topGO expects to be there. In this case the function would be MeSH.Dan.eg_dbconn, which obviously doesn't exist. But this doesn't preclude you from making one yourself!

As an example,

MeSH.Dan.eg_dbconn <- function() dbconn(MeSH.Dan.eg.db)

should fix your problem.

ADD COMMENTlink written 3.2 years ago by James W. MacDonald51k
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