我尝试用enrichGO和R.对拟南芥进行富集分析,但结果是空白的。是什么导致了这个结果?
> ego <- enrichGO(syn_block1_gene, OrgDb = "org.At.tair.db", keyType = "TAIR",ont = "BP")
> ego
#
# over-representation test
#
#...@organism Arabidopsis thaliana
#...@ontology BP
#...@keytype TAIR
#...@gene chr [1:754] "AT1G55230" "AT1G55240" "AT1G55380" "AT1G55390" "AT1G55420" ...
#...pvalues adjusted by 'BH' with cutoff <0.05
#...0 enriched terms found
#...Citation
Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
clusterProfiler: an R package for comparing biological themes among
gene clusters. OMICS: A Journal of Integrative Biology
2012, 16(5):284-287
> dotplot(ego)
> head(ego)
[1] ID Description GeneRatio BgRatio pvalue p.adjust
[7] qvalue geneID Count
<0 rows> (or 0-length row.names)
> as.data.frame(ego)[1,]
ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
NA <NA> <NA> <NA> <NA> NA NA NA <NA> NA
我相信syn_block1_gene
的数据是正确的。
发布于 2021-05-17 14:56:03
设置/包括参数pAdjustMethod = "none"
、pvalueCutoff = 1
和qvalueCutoff = 1
。
https://stackoverflow.com/questions/67571127
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