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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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OrgDb for maize #687

Open enriquepola1996 opened 2 months ago

enriquepola1996 commented 2 months ago

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 commented 2 months ago

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

Please have a look at one of my previous posts for some code to analyze an ensembl-based dataset: https://github.com/YuLab-SMU/clusterProfiler/issues/588#issuecomment-1600652905

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