enrichGO from DOSE, clusterprofiler is returning empty result.
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@kirannbishwa01-12980
Last seen 4.2 years ago

I am trying to use enrichGO function from clusterProfiler package. All is good except that my results are empty.

# for significant genes

> sig.foldChangesAbv2 %>% length()
[1] 244

> sig.foldChanges %>% head(5)
[1] "NA1"       "AT1G64640" "AT1G64630" "AT1G64625" "NA3"

# for universal genes

> length(names(foldChanges))
[1] 1761

> foldChanges %>% head(5)
       NA1  AT1G64720  AT1G64710  AT1G64700  AT1G64690
-2.2955229  0.6501073  0.7451122  0.6378277 -0.9689359

 

ego <- enrichGO(gene = sig.foldChangesAbv2.5 ,
                universe = names(foldChanges),
                keyType = "TAIR",
                OrgDb = org.At.tair.db,
                ont = "BP",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.1,
                qvalueCutoff  = 0.5,
                readable = TRUE)

> head(ego)
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust   
[7] qvalue      Count      
<0 rows> (or 0-length row.names)

Why is my result just empty? Is it because there are very few genes belonging to any GO category? or is the problem because I am using `Arabidopsis` database?

 

The `GO Classification` is working totally fine though.

> ggo <- groupGO(gene = names(foldChanges),
+                OrgDb = org.At.tair.db, keytype = "TAIR", ont = "BP",
+                level = 3, readable = TRUE)

> ggo
GO BP Profiles at level 3 of 1761 Arabidopsis thaliana genes


> head(ggo, 5)
                   ID                              Description Count GeneRatio
GO:0019953 GO:0019953                      sexual reproduction    20   20/1761
GO:0019954 GO:0019954                     asexual reproduction     0    0/1761
GO:0022414 GO:0022414                     reproductive process   147  147/1761

 

 

 

DOSE clusterprofiler annotation gene ontology gene set enrichment • 2.2k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 23 days ago
China/Guangzhou/Southern Medical Univer…
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Hello, this link is broken. Is there an updated link? I currently have the exact same issue. Thank you.

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