topGO analysis "MF" term error GenTable function

Question

[Luisa]

Hi all, I am using topGO in R to get GO terms from a set of genes.

example of some entries in my gene list: gene_list_ua COBS01388 COBS01391 COBS01392 COBS01392 COBS01392 COBS01392 COBS01392 COBS01393 COBS01395 COBS01396 0 0 0 0 0 0 0 0 0 0 Levels: 0 1

ontology_type = "MF" GO_data_ua_mf <- new("topGOdata", description="GO_Enrichment", ontology=ontology_type, allGenes=gene_list_ua, annot = annFUN.gene2GO, gene2GO=universe)

GO_data_ua_mf

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

Description:

• GO_Enrichment

  Ontology:

• MF

  17639 available genes (all genes from the array):

• symbol: COBS00002 COBS00003 COBS00004 COBS00004 COBS00005 ...

• 1524 significant genes.

  15720 feasible genes (genes that can be used in the analysis):

• symbol: COBS00002 COBS00003 COBS00004 COBS00004 COBS00006 ...

• 1359 significant genes.

  GO graph (nodes with at least 1 genes):

• a graph with directed edges
• number of nodes = 1299
• number of edges = 1691

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

result_topGO_w01_ua_mf <- runTest(GO_data_ua_mf, algorithm = "weight01", statistic = "fisher") result_topGO_w01_ua_mf

Description: GO_Enrichment Ontology: MF 'weight01' algorithm with the 'fisher' test 1299 GO terms scored: 28 terms with p < 0.01 Annotation data: Annotated genes: 15720 Significant genes: 1359 Min. no. of genes annotated to a GO: 1 Nontrivial nodes: 341

result_table_w01_ua_mf <- GenTable(GO_data_ua_mf, Fisher = result_topGO_w01_ua_mf, orderBy = "Fisher", ranksOf = "Fisher", topNodes = numSigGenes(GO_data_ua_mf))

Error in data.frame(infoMat, annoStat, apply(l, 2, format.FUN, dig = 2, : arguments imply differing number of rows: 1359, 1299 In addition: Warning message: In .genesInNode(graph(object), whichGO) : Nodes not present in the graph:NANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANANA

I don't get an error if I use "BP" and "CC" in the lines above.

R.version platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 1.2

topGO version 2.46.0 BiocManager version 1.30.16

What could be happening? I do not think the number of nodes and significant genes need to be the same as before it worked with BF and CC.

Thanks for your help!

Luisa

Answer 1

[sgallaher03]

Hi Luisa,

It may be that there are NA values in the dataframe. Can you remove any NAs present and see if you are getting the same error?

Thanks

Answer 2

[Luisa]

Hi Sarah,

The both objects used (S4 object of class topGOdata and S4 object of class topGOresult), do not have NAs. Not that I could find. For example:

sum(is.na(GO_data_ua_mf@allScores)) [1] 0 sum(is.na(GO_data_ua_mf@feasible)) [1] 0 sum(is.na(result_topGO_w01_ua_mf@score)) [1] 0

Neither the gene list: sum(is.na(gene_list_ua)) [1] 0

And the NANAs problem is a warning but not the error itself. Should I look somewhere else?

Thanks, Luisa