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.
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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?
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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
