Re: [R] How to create probeAnno object?
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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[R] How to create probeAnno object?
Hi, I want to use segChrom() method in tilingArray package. For that I need to create a probeAnno object. I could not find much much info by ?probeAnno. I need help in creating probeAnno object. Snap shot of the file(.txt): chr1 2500014 2500038 + 0.232689943122845 chr1 2500039 2500063 + 2.60502410304227 chr1 2500062 2500086 + 0.0756595313279895 chr1 2500080 2500104 + 0.78574617788405 chr1 2500122 2500146 + 0.57901385309105 chr1 2500143 2500167 + 0.443992729102625 chr1 2500163 2500187 + 0.538200424867007 chr1 2500183 2500207 + 1.50024545788701 chr1 2500205 2500229 + 0.152549915278444 Thanks in advance. Regards, Ambuj A Thacker The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to open .rda file in R
Hi Steve,
It worked!! Thank you very much..
Regards,
Ambuj A Thacker
--- On Fri, 22/1/10, Steve Lianoglou wrote:
From: Steve Lianoglou
Subject: Re: [R] How to open .rda file in R
To: "AMBUJ"
Cc: r-help@r-project.org
Date: Friday, 22 January, 2010, 12:30 AM
Hi,
1. Please keep replies on list -- note that you have to click "reply all", not
just "reply"
2. For your new problem:
On Thu, Jan 21, 2010 at 1:22 PM, AMBUJ wrote:
Hi Steve,
Thankyou for the reply. I still did not get the data from the file.I
executed the following commands:
> vars<-load('~/523/Data.rda')
> vars
[1] "seg_vegNew"
>print(seg_vegNew)
Am I doing some thing wrong here? Thanks in advance.
You just have to notice hat `seg_vegNew` is an environment ... it probably is
holding vars in it that I guess you're interested, see ?new.env
Try to "ls(seg_vegNew)"
You should see a list of variables in it ... say "x" was one of them, one way
that you can then get access to it is like so:
R> my.x <- get('x', seg_vegNew)
Now you can access 'my.x' as normal ...
Does that help?-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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[[alternative HTML version deleted]]
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] How to open .rda file in R
Hi, I have a file containing gene expressions written using the tillingArray package. I used load() and attach() to get the data into R. Both of them works fine. Now I want to see the contents of the file. How can I see the contents of the file? Thankyou for your time. Regards, Ambuj The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
