Hi.
I know that that error message is not very informative here, but you
get the error because (i) you are merging arrays from two different
chip types and (ii) there are no samples that have the same name (cf.
http://aroma-project.org/node/77) in two sets. That is, you have
> Chip type #1 of 2 ('Mapping250K_Sty'):
> Names: X0283_Sty250, X0288_Sty250, ..., X8390_Sty250
> Chip type #2 of 2 ('Mapping250K_Nsp'):
> Names: X0283_Nsp250, X0288_Nsp250, ..., X8390_Nsp250
The aroma pipeline infers which arrays are for the same sample by
their names. Note that "X0283_Sty250" and "X0283_Nsp250" are not the
same name. In order for aroma to match the "X0283" part of these
strings you can use so called fullname translators that are functions
that translates them on the fly (so you do not have to rename the
actual files). For example, you could just do:
fnt <- function(names, ...) { gsub("_", ",", names, fixed=TRUE); };
# fnt("X0283_Sty250") => "X0283,Sty250"
setFullNamesTranslator(cesNs[[1]], fnt);
setFullNamesTranslator(cesNs[[2]], fnt);
before doing glad <- GladModel(cesNs).
For more information on fullnames translators, see how-to page 'Use
fullname translators to rename data files'
[http://aroma-project.org/howtos/setFullNamesTranslator].
Hope this helps
Henrik
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)
>
>
>> 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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