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 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/
