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Question: topGO analysis runTest: non-numeric argument to binary operator
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gravatar for Dave Th.
9 weeks ago by
Dave Th.0
Dave Th.0 wrote:

Dear all,

I'm trying to analyze my microarray data using limma and topGO. So far, after testing with limma, there are  75 significant genes, 8 upregulated and 67 downregulated genes. Now I would like to run topGO to find out which GO terms are enriched.

  1. When I tried with the whole set of 75 sig. genes, everything works fine. I got top 20 GO Terms but I don't know which GO term is up or down. How can I get this information?

  2. Then, I separated the sig. genes into 2 group (up and down) based on their logFC. With them same codes I used for the whole data set, the downregulated group is ok, I also got the top GO terms.  But the upregulated group (8 genes) cannot perform the Fisher test, it said: "Error in anno * expect : non-numeric argument to binary operator". Anyone knows what happened?

 Thank you.

 

204810_s_at 1158 CKM -7.82322 7.739031 -23.179 5.89E-07 0.006849 5.283822
208004_at 58503 OPRPN -6.4044 7.315894 -22.3978 7.18E-07 0.006849 5.204462
205177_at 7135 TNNI1 -8.30422 6.045471 -22.2198 7.52E-07 0.006849 5.185491

> upGOdata

------------------------- topGOdata object -------------------------

 Description:

   -  Scar formation BP 

 Ontology:

   -  BP 

 8 available genes (all genes from the array):

   - symbol:  215461_at 215787_at 1562573_at 1560464_at 1552763_at  ...

   - score :  1.731603e-05 2.123974e-05 2.4986865e-05 2.6593393e-05 3.0812251e-05  ...

   - 8  significant genes. 

 8 feasible genes (genes that can be used in the analysis):

   - symbol:  215461_at 215787_at 1562573_at 1560464_at 1552763_at  ...

   - score :  1.731603e-05 2.123974e-05 2.4986865e-05 2.6593393e-05 3.0812251e-05  ...

   - 8  significant genes. 

 GO graph (nodes with at least  10  genes):

   - a graph with directed edges

   - number of nodes = 0 

   - number of edges = 0 

------------------------- topGOdata object -------------------------

> resultFisher <- runTest(upGOdata, algorithm = "classic", statistic ="fisher")


Error in anno * expect : non-numeric argument to binary operator

ADD COMMENTlink written 9 weeks ago by Dave Th.0
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