Question: Different geneset same p-values in topGO
0
gravatar for Lluís Revilla Sancho
2.8 years ago by
European Union
Lluís Revilla Sancho510 wrote:

I have performed the "elim" (It happens the same with the weight01 algorithm) test in the same gene universe selecting different genes. However the p-values are the same even if different number of genes are indicated as significant for the same GO.ID. Here is a reproducible example:

library("topGO")
data(GOdata)
geneSelectionFun(GOdata) <- function(x) {x == 1L}
GOdata
resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes1 <- GenTable(GOdata, resultKS.elim)
geneSelectionFun(GOdata) <- function(x) {x > 0.5}
GOdata
resultKS.elim2 <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes2 <- GenTable(GOdata, resultKS.elim2)

In this case the GO terms with ID GO:0007067, GO:0051301, GO:0000087, GO:0022403, GO:0000226 have different number of "Significant" genes annotated, thus I expect to have a different p-value but it isn't reported different in each result table. Which makes me think if the elim algorithm is independent of the selected genes. Could the maintainer (or anyone else) explain it to  me?

topgo bug • 403 views
ADD COMMENTlink written 2.8 years ago by Lluís Revilla Sancho510

Probably related if I set another ontology the same GO terms (they should be different!!) and p-values are used when retrieving scores:

ontology(GOdata) <- "CC"

resultKS.elim3 <- runTest(GOdata, algorithm = "elim", statistic = "ks")

GenTable(GOdata, resultKS.elim3)

       GO.ID Term Annotated Significant Expected result1
1  GO:0007067 <NA>       183          86    84.59 2.9e-09
2  GO:0051301 <NA>       126          67    58.25 9.6e-06
3  GO:0008202 <NA>         9           8     4.16 0.00084
4  GO:0022900 <NA>         8           7     3.70 0.00120
5  GO:0009267 <NA>         6           6     2.77 0.00157
6  GO:0007565 <NA>         8           7     3.70 0.00181
7  GO:0000087 <NA>       188          91    86.91 0.00187
8  GO:0006636 <NA>         9           7     4.16 0.00322
9  GO:0022403 <NA>       192          95    88.75 0.00414
10 GO:0000226 <NA>        30          21    13.87 0.00545
ADD REPLYlink written 2.8 years ago by Lluís Revilla Sancho510
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