Hi,
I am encountering a strange occurrence with topGO and I don't understand some of the output I am getting.
Using the following relatively straight forward code
myGOdata <- new("topGOdata", description="My project", ontology="BP", allGenes=geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO)
resultFisherweight <- runTest(myGOdata, algorithm="weight01", statistic="fisher")
resultFisherclassic <- runTest(myGOdata, algorithm="classic", statistic="fisher")
resultFisherelim <- runTest(myGOdata, algorithm="elim", statistic="fisher")
sig.tab <- GenTable(myGOdata, pFisweight = resultFisherweight,pFisClassic=resultFisherclassic, pelimFisher=resultFisherelim, topNodes = length(go), numChar=1000)##for all of the GO terms
goid<- "GO:0050890"
termStat(myGOdata, goid)
I generated output that looks like this. Note the 2 significant genes
Annotated Significant Expected
GO:0050890 164 2 1.34
From some work out of R* and topGO, i find that the 2 significant genes (out of 88 possible ones) are: Ccalc.v3.00391 Ccalc.v3.14166
Now, look at the associated GO terms for each of these genes (below). The problem is that GO:0050890 is missing from Ccalc.v3.00391, but is present in Ccalc.v3.14166. But, topGO seems to detect GO:0050890 in Ccalc.v3.00391 even though it is not there! Why? Is this an error on topGO?
There are similar GO terms within Ccalc.v3.00391, like GO:0050896, but topGO shouldn't be detecting this, right?
Ccalc.v3.00391 GO:0000139, GO:0000166, GO:0001664, GO:0002027, GO:0002031, GO:0003674, GO:0003676, GO:0003677, GO:0003697, GO:0003700, GO:0003723, GO:0003724, GO:0003735, GO:0003887, GO:0003924, GO:0004190, GO:0004386, GO:0004519, GO:0004527, GO:0004674, GO:0005085, GO:0005102, GO:0005198, GO:0005509, GO:0005515, GO:0005524, GO:0005576, GO:0005634, GO:0005667, GO:0005730, GO:0005737, GO:0005743, GO:0005770, GO:0005773, GO:0005774, GO:0005783, GO:0005789, GO:0005791, GO:0005794, GO:0005829, GO:0005834, GO:0005840, GO:0005886, GO:0005887, GO:0005975, GO:0006260, GO:0006261, GO:0006269, GO:0006270, GO:0006310, GO:0006325, GO:0006342, GO:0006355, GO:0006364, GO:0006412, GO:0006417, GO:0006468, GO:0006508, GO:0006865, GO:0006914, GO:0007007, GO:0007154, GO:0007165, GO:0007186, GO:0007188, GO:0007219, GO:0007220, GO:0007411, GO:0007412, GO:0007417, GO:0007422, GO:0007480, GO:0007614, GO:0008053, GO:0008083, GO:0008152, GO:0008168, GO:0008233, GO:0008306, GO:0008408, GO:0008593, GO:0008833, GO:0009295, GO:0015074, GO:0015677, GO:0016020, GO:0016021, GO:0016032, GO:0016055, GO:0016209, GO:0016301, GO:0016310, GO:0016319, GO:0016324, GO:0016485, GO:0016491, GO:0016539, GO:0016740, GO:0016757, GO:0016779, GO:0016787, GO:0016788, GO:0016798, GO:0016813, GO:0016874, GO:0018024, GO:0018142, GO:0019001, GO:0019028, GO:0019033, GO:0019050, GO:0019062, GO:0019068, GO:0019076, GO:0019835, GO:0020002, GO:0030036, GO:0030424, GO:0030426, GO:0030430, GO:0030683, GO:0031151, GO:0031234, GO:0031532, GO:0031648, GO:0031683, GO:0032259, GO:0032974, GO:0033644, GO:0034729, GO:0035025, GO:0035333, GO:0035556, GO:0035641, GO:0039573, GO:0039664, GO:0039678, GO:0039693, GO:0042025, GO:0042407, GO:0042803, GO:0042981, GO:0043409, GO:0044659, GO:0045746, GO:0045751, GO:0045879, GO:0045887, GO:0046718, GO:0046729, GO:0046797, GO:0046798, GO:0046872, GO:0046983, GO:0048190, GO:0048260, GO:0050728, GO:0050770, GO:0050790, GO:0050896, GO:0051726, GO:0051920, GO:0055036, GO:0055037, GO:0055085, GO:0060158, GO:0060189, GO:0061617, GO:0070765, GO:0071627, GO:0071772, GO:0071897, GO:0075521, GO:0075606, GO:0090305, GO:0098003, GO:0098015, GO:0098024, GO:0098671, GO:0098869, GO:0098994, GO:0099001, GO:0099002, GO:0120177
Ccalc.v3.14166 GO:0000166, GO:0003677, GO:0003697, GO:0003723, GO:0003824, GO:0004045, GO:0004176, GO:0004252, GO:0004519, GO:0004617, GO:0005198, GO:0005388, GO:0005524, GO:0005576, GO:0005634, GO:0005737, GO:0005768, GO:0005769, GO:0005798, GO:0005886, GO:0005905, GO:0006210, GO:0006212, GO:0006259, GO:0006260, GO:0006281, GO:0006310, GO:0006508, GO:0006564, GO:0006816, GO:0006974, GO:0007399, GO:0008094, GO:0008233, GO:0008652, GO:0009267, GO:0009432, GO:0009986, GO:0016020, GO:0016021, GO:0016491, GO:0016616, GO:0016627, GO:0016740, GO:0016787, GO:0016788, GO:0017113, GO:0030426, GO:0031410, GO:0042995, GO:0043204, GO:0046872, GO:0050485, GO:0050890, GO:0051287, GO:0051536, GO:0055037, GO:0070403, GO:0070588, GO:0090305, GO:0140603
