[aroma.affymetrix] GLAD not producing output

2010-09-07 Thread Gene
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_0.1.7affxparser_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_0.3.6R.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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Re: [aroma.affymetrix] GLAD not producing output

2010-09-07 Thread Pierre Neuvial
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.


 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/