[BioC] topGO issues

[kaushal Raj Chaudhary [guest]]

Hi List,

I have illumina expression data from mouse chip.  I was using topGO package with probe id and P values .I am not sure if I can use hgu95av2.db for annotation.  I encountered follwing error.  I appreciate your help.  Thank you.

 -- output of sessionInfo(): 

 data1=read.csv ("go.csv", header=T)  
data1    
       ProbeID           p
1   2810273 0.022920083
2   5720014 0.042961586
3   2600424 0.025965275
4   3520176 0.032705434
5   1240739 0.000668000
6   1190735 0.016157765
…………………………………………..
rn<-paste(data1[,1], sep="")
P_values=data1[,-1]
names(P_values)<-rn  ####creating named vectors
P_values    ### this contains probeID with corresponding p-values

2810273     5720014     2600424     3520176     1240739     1190735 
0.022920083 0.042961586 0.025965275 0.032705434 0.000668000 0.016157765 
    4280164     2480441     5870504     5390019     5220576     4060465 
0.002103902 0.017717950 0.034700550 0.021078015 0.012964631 0.014807984 
    4050653     1470619     4610131     2650730     2690035     4670288 
0.036829505 0.001426032 0.010399277 0.010104929 0.003046091 0.005084754 
    4900064     6400377     5560204     2120377     4150037     1240370 
0.004906018 0.020934649 0.020285547 0.009254484 0.038157470 0.001123237 
    2350068     3400246     4730630     3850167     4860048     2000674
…………………………………………………………………………………………..
affyLib <- paste(annotation (ALL), "db", sep = ".")
library(package = affyLib, character.only = TRUE)
[1] "hgu95av2.db"
sum(topDiffGenes(P_values))
75

sampleGOdata <- new("topGOdata",
 description = "Simple session", ontology = "BP",
 allGenes = P_values, geneSel = topDiffGenes,
 nodeSize = 10,
 annot = annFUN.db, affyLib = affyLib)


Building most specific GOs .....        ( 0 GO terms found. )

Build GO DAG topology ..........        ( 0 GO terms and 0 relations. )
Error in if (is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  : 
  missing value where TRUE/FALSE needed


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