Hi,
On Wed, Apr 18, 2012 at 3:05 PM, Sathish Periyasamy <
sathish.periyas...@gmail.com> wrote:
> I am getting the following error segs <- getSegments(fit); The error
> output is as follows:
>
> Please assist me in solving the following error.
>
> regards
>
> chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs
> tcnNbrOfHets
> 1 25 1 1 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
> 1 1598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
> 1 25 1 1 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
> 1 1598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
> 1 25 1 1 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
> 1 1598 16148 1 0.3252 0.6596 1.295 chromosome tcnId dhId
> tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
> 1 25 1 1 1598 16148 26 1.955 26
> 1
> dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
> 1 1598 16148 1 0.3252 0.6596 1.29520120418 15:49:56|
> Chromosome #25 ('Chr25') of 25...done20120418 15:49:56| Merging
> (independently) segmented chromosome...Error: cannot allocate vector of size
> 17.3 Mb
>
>
The first error is actually here (just above).
17.3 Mb is really not much, and should not be a problem. Maybe you have
large objects in your R session. Can you try again from a fresh R session ?
Another possibility is that you have other programs than R taking all your
RAM.
More below.
> In addition: There were 50 or more warnings (use warnings() to see the first
> 50)20120418 15:50:43| Merging (independently) segmented
> chromosome...done20120418 15:50:43| Segmenting multiple
> chromosomes...done20120418 15:50:43|Segmenting paired tumor-normal signals
> using Paired PSCBS...done> > segs <- getSegments(fit);Error in
> UseMethod("getSegments") :
> no applicable method for 'getSegments' applied to an object of class
> "function"
>
>
Your 'fit' object was not created because of the above error, hence this
second error ('fit' is also a function in your R environment).
Cheers,
Pierre
> #segs <- getSegments(fit);> print(segs);Error in print(segs) : object 'segs'
> not found> #help("segmentByPairedPSCBS", package="PSCBS");> > pairName <-
> paste(pair, collapse="vs");> chrTag <- sprintf("Chr%s",
> seqToHumanReadable(getChromosomes(fit)));Error in UseMethod("getChromosomes")
> :
> no applicable method for 'getChromosomes' applied to an object of class
> "function"> > toPNG(pairName, tags=c(chrTag, "PairedPSCBS"), width=840,
> aspectRatio=0.6, {+ plotTracks(fit);+ });Error in paste(c(name, tags),
> collapse = ",") : object 'chrTag' not found
>
> >
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
