enrichGO from DOSE, clusterprofiler is returning empty result.
1
1
Entering edit mode
@kirannbishwa01-12980
Last seen 5.7 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 • 3.4k views
ADD COMMENT
1
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 6 months ago
China/Guangzhou/Southern Medical Univer…
ADD COMMENT
0
Entering edit mode

Hello, this link is broken. Is there an updated link? I currently have the exact same issue. Thank you.

ADD REPLY

Login before adding your answer.

Traffic: 589 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6