[BioC] goHyperG generates GO links at arrays.ucsf.edu with wrong perl script,

[Saurin Jani]

Dear BioC,

Here are the versions I have for packages and R. I use
affy data. e.g. here, moe430a GeneChip. I have also
attached HTML file(which links to
http://arrays.ucsf.edu/cgi-bin/oligo_db.pl) along with
this email, Please take a look of that. 

> package.version("affy")
[1] "1.6.7"
> package.version("GO")
[1] "1.8.2"
> package.version("GOstats")
[1] "1.1.3"
> package.version("moe430a")
[1] "1.8.5"
> getRversion()
[1] ‘2.2.0’

>myGOreports_1(myDEGenes,chiptype,"GeneOntology_Cellular_Component_Report.html","GeneOntology_Molecular_Function_Report.html","GeneOntology_BiologicalProcess_Report.html");
#---------------------------------------
# Gene Ontology function 
#---------------------------------------

myGOreports_1 <-
function(Gnames,chiptype,CCfile,MFfile,BPfile)
{ 

  myLL <- getLL(Gnames,chiptype);
  myUNQLL  <-
as.character(na.omit(unique(unlist(myLL))));

  # for CC Go report
  #-----------------
  myGOCC <-  GOHyperG(myUNQLL, lib = chiptype,
what="CC");
  DECCnodes = names(myGOCC$intCounts);
  CCTERMS <- as.matrix(unlist(getGOTerm(DECCnodes)));
  CC_Genes <- as.matrix(as.vector(myGOCC$intCounts));
  CC_pvalues <-  as.vector(myGOCC$pvalues);
  CC_AllGenes <-
as.matrix(as.vector(myGOCC$goCounts));

  GOtable_CC <-
as.table(cbind(DECCnodes,CCTERMS,CC_Genes,CC_pvalues,CC_AllGenes));
  colnames(GOtable_CC) <- c("GO ID","GO TERM :
Cellular Component ",
            "No of DE Genes ","p-values"," Total No of
Genes from Array Chip ");
  table2html(GOtable_CC,filename = CCfile,
     title = " Gene Ontology: Cellular Component
Report",disp = c("File"));

  # for MF Go report
  #-----------------
  myGOMF <-  GOHyperG(myUNQLL, lib= chiptype,
what="MF");
  DEMFnodes = names(myGOMF$intCounts);
  MFTERMS <- as.matrix(unlist(getGOTerm(DEMFnodes)));
  MF_Genes <-  as.vector(myGOMF$intCounts);
  MF_pvalues <-  as.vector(myGOMF$pvalues);
  MF_AllGenes <-
as.matrix(as.vector(myGOMF$goCounts));

  GOtable_MF <-
as.table(cbind(DEMFnodes,MFTERMS,MF_Genes,MF_pvalues,MF_AllGenes));
  colnames(GOtable_MF) <- c("GO ID","GO Term :
Molecular Function ",
           "No of DE Genes ","p-values"," Total No of
Genes from Array Chip ");

  table2html(GOtable_MF,filename = MFfile,title =
    " Gene Ontology: Molecular Function  Report",disp
= c("File"));

  # for BP Go report
  #-----------------
  myGOBP <-  GOHyperG(myUNQLL, lib=chiptype,
what="BP");
  DEBPnodes = as.vector(names(myGOBP$intCounts));
  BPTERMS <- as.vector(unlist(getGOTerm(DEBPnodes)));
  BP_Genes = as.vector(myGOBP$intCounts);
  BP_pvalues <-  as.vector(myGOBP$pvalues);
  BP_AllGenes <-
as.matrix(as.vector(myGOBP$goCounts));

  GOtable_BP <-
as.table(cbind(DEBPnodes,BPTERMS,BP_Genes,BP_pvalues,BP_AllGenes));
  colnames(GOtable_BP) <- c("GO ID","GO Term :
Biological Process ",
    "No of DE Genes ","p-values"," Total No of Genes
from Array Chip ");
  table2html(GOtable_BP,filename = BPfile,
    title = " Gene Ontology: Biological Process
Report",disp = c("File"));

}#myGOreport_1

#---------------------------------------
# End of Gene Ontology function 
#---------------------------------------


Please let me know, if I can add links while
generating GO html file. 

Thank you so much,
Saurin


--- Robert Gentleman <rgentlem at fhcrc.org> wrote:

> Can you please give enough of an example that we can
> test this. The 
> output of sessionInfo or enough package version
> information that there 
> is some chance that someone could help you?
> 
> 
> Saurin Jani wrote:
> > Dear BioC,
> > 
> > We have noticed that the GOHyperG function within
> the
> > GOstat package generates HTML links to GOIDs that
> have
> > NO associated information. A typical link is
> >
>
http://arrays.ucsf.edu/cgi-bin/oligo_db.pl?oligo=GO:0030111.
> > Is there a fix for this problem? 
> > 
> > Thank you,
> > Saurin
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
> 


		
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