Hi,
correct, process() of ChromosomeExplorer will generate a regions.xls
file *based on the settings of the most recent call overwriting any
earlier versions of the file*.
A solution for your case, where you process each array independently,
is to create a separate "regions" file for each array. This can be
done by:
fit(cbs, arrays=array, chromosomes=1:23, verbose=verbose);
pathname <- writeRegions(cbs, arrays=array, chromosomes=1:23,
oneFile=FALSE, verbose=verbose);
print(pathname);
## [1]
cbsData/GSE8605,ACC,-XY,RMA,+300,A+B,FLN,-XY/Mapping10K_Xba142/GSM226868,regions.xls
Note that the tab-delimited file is stored under cbsData/ (and not
under reports/). Also ChromosomeExplorer is not involved here. Thus,
unless you want the ChromosomeExplorer report/image files, you can do
the above instead. writeRegions() will call fit(), if not already
done, but it is better style to be explicit about fit(), especially in
scripts.
Hope this helps
Henrik
On Fri, Jan 7, 2011 at 7:56 PM, Kai <wangz...@gmail.com> wrote:
> Hi Henrik,
>
> In a previous post I learned from you that I can run CBS segmentation
> on one sample at a time and submit multiple runs at the same time to a
> computing cluster to increase the speed of processing. This has been
> working quite well until I realized that the "regions.xls" under the
> CbsModel folder and ChromsomeExplorer folder got messed up. I guess
> this was due to multiple threads writing to this file simultaneously
> instead of sequentially. So I was wondering whether there is a way to
> get around of this, either by writing all regions from all samples
> again after all samples are processed, or having each sample outputs
> its segments into different files.
>
> My current process is like the following:
>
> library("aroma.core");
> verbose <- Arguments$getVerbose(-4, timestamp=TRUE);
> arrays <- 1; # Change for different hosts
> ds <- AromaUnitTotalCnBinarySet
> $byName("dataset,paired",chipType="HumanOmni1-Quad");
> cbs <- CbsModel(ds, min.width=5, undo.splits="sdundo", undo.SD=1);
> cbs$.calculateRatios <- FALSE;
> ce <- ChromosomeExplorer(cbs);
> process(ce, arrays=arrays, chromosomes=c(1:23), verbose=verbose);
>
> And I split my datasets of ~300 samples into individual process and
> submit them simultaneously to our computing cluster.
>
> Thank you very much for your help on this.
>
> Best,
> Kai
>
> --
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