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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