[R] How to create probeAnno object?
mtmorgan at fhcrc.org
Sat Feb 13 16:30:24 CET 2010
On 02/11/2010 08:03 PM, AMBUJ wrote:
> Thank you Viviana for the description to create probeAnno object. The below link was very helpful:
This is just the help page for one of Ringo's classes. It's available in
Have you looked at
? 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
and always useful to include the output of
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
> 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.
calling 'new' without naming the second and subsequent arguments is not
likely to create the object you expect. Maybe
map = new("environment",
Here you're probably aiming for something like
new("probeAnno", map=map, arrayName=arrrayName, genome=genome)
> 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.
> A 'probeAnno' object holding the mapping between reporters and genomic positions.
> Chromosomes: 1
> Microarray platform: S.Pombe
> Genome: genome
> 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.
> Ambuj A Thacker
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
More information about the R-help