Question

compareCluster error: On clusterProfiler DEGs enrichments analysis

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Entering edit mode

tpm • 0

@tpm-23631

Last seen 3.5 years ago

Netherlands

I am working on Clusterprofiler. I am comparing 4 gene sets. I encountered an error, and I am trying to figure out what could be the problem when I run the compareCluster function. I do not know how I can solve this issue.

> lapply(LISTcutoff5, head)
$EC11WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

$EC12WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

$EC17WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

$EC17WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

When I run this code:

 ckk50 <- compareCluster(geneCluster = LISTcutoff5, fun = "enrichGO", OrgDb = "org.EcK12.eg.db",ont="BP")

I get this error:

Error in `levels<-`(`*tmp*`, value = as.character(levels)) : 
  factor level [4] is duplicated

clusterProfiler Bioconductor R DEGs • 1.1k views

ADD COMMENT • link 4.5 years ago tpm • 0

0

Entering edit mode

I realized the mistake, which was here 'EC17WT' as I have identical names. I had to change one of them: So not like this

$EC17WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

$EC17WT
[1] "947315" "944895" "947758" "947761" "946796" "948517"

but like this:

    $EC17WT
    [1] "947315" "944895" "947758" "947761" "946796" "948517"

    $EC18WT
    [1] "947315" "944895" "947758" "947761" "946796" "948517"

Being new on R has lots of challenges and embarrassingly, it can be a mere typo.

Thanks in advance.

ADD REPLY • link 4.5 years ago tpm • 0