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Error when runing dotplot with enrichGO results

I used to run the exactly same commands in Rstudio and no errors occured.

ego <- enrichGO(gene=gene_EntrezID,OrgDb = org.Hs.eg.db,keytype = "ENTREZID", ont="BP",readable = T,pvalueCutoff = 0.001,qvalueCutoff = 0.001)
dotplot(ego,colorBy = "pvalue",showCategory = 10)

But now this error jumps out:

Error in unique.default(x, nmax = nmax) : 
  unique() applies only to vectors

I can't find out the reason, could someone help me please ? Thx !

clusterprofier dotplot
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updated by Anthony • Anthony • written by dingailuma • dingailuma

Another question, anyone know how to set compareCluster results readable ? (I mean transfer ENTREZID to GENE SYMBOL) ? Thx again !

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written by dingailuma • dingailuma

Hi,

I never used this package, but looking at your error only, it seems to indicate that your "ego" object is not a vector. Can you see what "ego" is?

head(ego)

or

str(ego)
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written by Benn Benn

I found if I use plot() instead of dotplot() , then no errors . Wierd ! Maybe some bugs when authors updating the clusterprofiler package.

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written by dingailuma • dingailuma

or class(ego). My money is on an unexpected factor.

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written by WouterDeCoster WouterDeCoster

1 answer

To avoid the error, use DOSE::dotplot instead of dotplot.

The error occurs when you use the lattice package, which may have been loaded by another package you were using:

The following object is masked from ‘package:clusterProfiler’:

    dotplot
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written by Anthony • Anthony

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