[R] How to create probeAnno object?

[AMBUJ]

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

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


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