Question: RamiGO: getAmigoTree producing internal server errors
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gravatar for Asta Laiho
4.1 years ago by
Asta Laiho120
Finland
Asta Laiho120 wrote:

 

 

Hi,

 

 

I have been using RamiGO for producing GO graphs for quite a while but recently it has started crashing with internal server errors. The problem seems to be related to certain GO terms (many of them actually).

 

List of goIDs and associate pvalues:
 

> goIDs 

 [1] "GO:0003735" "GO:0004713" "GO:0008022" "GO:0051020" "GO:0005085"

 [6] "GO:0017137" "GO:0031267" "GO:0003714" "GO:0016758" "GO:0017016"

[11] "GO:0005083" "GO:0019838" "GO:0005178" "GO:0005088" "GO:0004721"

[16] "GO:0051082" "GO:0004725" "GO:0008017" "GO:0016779" "GO:0004714"

[21] "GO:0016741" "GO:0008168" "GO:0031625" "GO:0044389" "GO:0016829"

[26] "GO:0019199" "GO:0043021" "GO:0072509" "GO:0000287" "GO:0016853"

[31] "GO:0005099" "GO:0035091" "GO:1901681" "GO:0003729" "GO:0003725"

[36] "GO:0008376" "GO:0016747" "GO:0019902" "GO:0005262" "GO:0019903"

[41] "GO:0035254" "GO:0008013" "GO:0019205" "GO:0050662" "GO:0044325"

[46] "GO:0004518" "GO:0001076" "GO:0019003" "GO:0016831" "GO:0050660"

> pvalues

 [1] 0.000101 0.000101 0.000101 0.000101 0.000106 0.000119 0.000189 0.000369

 [9] 0.000392 0.000606 0.000833 0.000833 0.000899 0.000973 0.001510 0.001560

[17] 0.001860 0.002030 0.002110 0.002170 0.002170 0.002660 0.003300 0.003300

[25] 0.003700 0.003700 0.006010 0.006010 0.006040 0.008010 0.008030 0.008810

[33] 0.008890 0.009360 0.011200 0.012100 0.012100 0.012100 0.012500 0.013000

[41] 0.013500 0.013800 0.013800 0.013800 0.014000 0.014300 0.014700 0.014700

[49] 0.015900 0.016300

 

res <- getAmigoTree(goIDs, pvalues)

Error during wrapup: Internal Server Error


 

#Removing the problematic GO terms:

ind <- which(goIDs=="GO:0005099" | goIDs=="GO:0005083")

goIDs <- goIDs[-ind]

pvalues <- pvalues[-ind]

 

res <- getAmigoTree(goIDs, pvalues)

#after which the function works normally

So I have also found many other problematic GO terms and updating the GO.db does not seem to help. 

ramigo • 437 views
ADD COMMENTlink written 4.1 years ago by Asta Laiho120
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