[R] How to create probeAnno object?

Martin Morgan mtmorgan at fhcrc.org
Sat Feb 13 16:30:24 CET 2010

On 02/11/2010 08:03 PM, AMBUJ wrote:
> Hi,
>             Thank you Viviana for the description to create probeAnno object. The below link was very helpful:
>     http://svitsrv25.epfl.ch/R-doc/library/Ringo/html/probeAnnoClass.html

This is just the help page for one of Ringo's classes. It's available in
R with

  > library(Ringo)
  > ?probeAnno

Have you looked at

  > browseVignettes("Ringo")

? Ringo is a Bioconductor package so ask on the Bioconductor mailing list


Might as well include the maintainer in your email, since they're likely
to be the expert

  > packageDescription("Ringo")

and always useful to include the output of

  > sessionInfo()

to unambiguously report the version of R and Ringo you're using. A first
action is usually to update to the latest released R and corresponding
Bioconductor packages,


> I tried creating the object in the following ways where: startProbe & endProbe are the vectors which has the genomic start co-ordinates and end co-ordinates and index is a vector to store identifier of the probes. intensityData is the vector that stores data to be segmented
> Method 1.
>> map<-new("environment",startProbe,endProbe,index)

calling 'new' without naming the second and subsequent arguments is not
likely to create the object you expect. Maybe

  map = new("environment",
             startProbe=startProbe, endProbe=endProbe,


>> arrayName<-"2009_01_18_veg1028_w"
>> genome<-"genome"
>> probeAnnotation<-new("probeAnno",map,arrayName,genome)

Here you're probably aiming for something like

  new("probeAnno", map=map, arrayName=arrrayName, genome=genome)


>> segEnv<-segChrom(intensityData,probeAnno=probeAnnotation,chr="1",strands="+",nrBasesPerSegment=750)

> Running 'segment' on chromosome 1.+Error in mget(paste(chrstrd[j],
what, sep = "."), probeAnno) : second argument must be an environment

> Method 2.
>> pa3<-posToProbeAnno("~/523/POSFormat_tab.csv");Creating probeAnno mapping for chromosome 1 Done.
>> arrayName(pa3)<-"S.Pombe"
>> genome(pa3)<-"genome"
>> show(pa3)
> A 'probeAnno' object holding the mapping between reporters and genomic positions.
> Chromosomes: 1
> Microarray platform: S.Pombe 
> Genome: genome
>> segEnv<-segChrom(intensityData,probeAnno=pa3,chr="1",strands="+",nrBasesPerSegment=750)
> Running 'segment' on chromosome 1.+Error in mget(paste(chrstrd[j], what, sep = "."), probeAnno) :   second argument must be an environment
> Both the methods gave the same error "second argument must be an environment". I am unable to execute segChrom() of tilingArray package. Any sugetions would be helpful. Thanks in advance.
> Regards,
> Ambuj A Thacker
>       The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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