[BioC] topGO issues

[Marc Carlson]

Hi Raj,

The problem seems to be that instead of using the appropriate annotation 
package you are grabbing the one used by the ALL example object. As a 
1st step, you might want to look at our website and see if there is a 
different annotation package that better matches your array. You can see 
the list of packages on our website here:

http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData


Marc


On 09/11/2013 08:15 AM, kaushal Raj Chaudhary [guest] wrote:
> 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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