Hi Gene,
On Tue, Sep 7, 2010 at 4:38 PM, Gene <genetas...@gmail.com> wrote:
> I couldn't get any of the output methods to work to save my GLAD
> segmentation results (see output below). When I took a look at the
> auto-generated GLAD directory gladData/gsk,ACC,-XY,BPN,-XY,RMA,A
> +B,FLN,-XY/Mapping250K_Sty+Nsp, I saw that it was empty. I had been
> following along with the vignettes, so it's unclear to me what went
> wrong. If anyone can point out the problem, I would be very
> appreciative!
>
> Thanks.
>
>
>> glad <- GladModel(cesNs)
>
>> print(glad)
> GladModel:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Chip type (virtual): Mapping250K_Sty+Nsp
> Path: gladData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty+Nsp
> Number of chip types: 2
> Sample & reference file pairs:
> Chip type #1 of 2 ('Mapping250K_Sty'):
> Sample data set:
> CnChipEffectSet:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Path: plmData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty,monocell
> Number of arrays: 205
> Names: X0283_Sty250, X0288_Sty250, ..., X8390_Sty250
> Time period: 2010-08-23 14:55:28 -- 2010-08-23 14:56:57
> Total file size: 2940.06MB
> RAM: 0.58MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Reference data set/file:
> <average across arrays>
> Chip type #2 of 2 ('Mapping250K_Nsp'):
> Sample data set:
> CnChipEffectSet:
> Name: cgh
> Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Path: plmData/cgh,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Nsp
> Platform: Affymetrix
> Chip type: Mapping250K_Nsp,monocell
> Number of arrays: 205
> Names: X0283_Nsp250, X0288_Nsp250, ..., X8390_Nsp250
> Time period: 2010-08-25 02:24:26 -- 2010-08-25 02:25:37
> Total file size: 3230.09MB
> RAM: 0.58MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> Reference data set/file:
> <average across arrays>
> RAM: 0.00MB
>
>> str(glad)
> Classes 'GladModel', 'CopyNumberSegmentationModel',
> 'CopyNumberChromosomalModel', 'ChromosomalModel', 'Object' atomic
> [1:1] NA
> ..- attr(*, ".env")=<environment: 0x14f2a7408>
> ..- attr(*, "...instantiationTime")= POSIXct[1:1], format:
> "2010-09-07 16:18:09"
>
>> rawCNs <- extractRawCopyNumbers(glad, array=1, chromosome=1)
>
> Error in list(`extractRawCopyNumbers(glad, array = 1, chromosome = 1)`
> = <environment>, :
>
> [2010-09-07 16:37:33] Exception: Argument 'x' is of length 1 although
> the range ([0,0]) implies that is should be empty.
> at throw(Exception(...))
> at throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s
> at throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) im
> at getIndices.Arguments(static, ..., length = length)
> at getIndices(static, ..., length = length)
> at method(static, ...)
> at Arguments$getIndex(array, max = nbrOfArrays(this))
> at extractRawCopyNumbers.CopyNumberChromosomalModel(glad, array = 1,
> chromosom
> at extractRawCopyNumbers(glad, array = 1, chromosome = 1)
>
>
Did you fit the glad model before calling extractRawCopyNumbers, i.e.
fit(glad, verbose=verbose);
?
Pierre
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] RColorBrewer_1.0-2 GLAD_2.10.0
> aroma.affymetrix_1.7.0
> [4] aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0
> [7] aroma.core_1.7.0 aroma.light_1.16.0
> matrixStats_0.2.1
> [10] R.rsp_0.3.6 R.cache_0.3.0
> R.filesets_0.8.3
> [13] digest_0.4.2 R.utils_1.4.4
> R.oo_1.7.3
> [16] R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
>
> --
> 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.
>
>
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>
--
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
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