Henrik, you have come through for me again! Thanks for solving my problem.
Gene On Sep 8, 12:54 am, Henrik Bengtsson <h...@stat.berkeley.edu> wrote: > 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. > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://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. 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