OrgDb for maize

[enriquepola1996]

Hello,

I am trying to perform a GO analysis with clusterProfiler, however I am having problems with OrgDb because it is not supported, could anyone suggest something to resolve this?

#ORA
ora_analysis_BP <- enrichGO(
  gene = annot_diff$entrezgene_id,
  universe = annot_universe$entrezgene_id,
  OrgDb= ????,
  keyType = "ENTREZID",
  ont = "BP",
  pAdjustMethod = "BH",
  qvalueCutoff = 0.05,
  readable = TRUE,
  pool = FALSE
)

Update:

I solved my problem with AnnotationHub:

https://guangchuangyu.github.io/cn/2017/07/clusterprofiler-maize/#disqus_thread

Thanks.

[guidohooiveld]

Your post on the Bioconductor support forum originally revealed that your were using a dataset based on ensembl ids.

Please have a look at one of my previous posts for some code to analyze an ensembl-based dataset: #588 (comment)

Note that you will have to modify it slightly because I used it to analyze an ensembl-based tomato dataset.