Hi.
On Mon, Jul 4, 2016 at 12:43 AM, roman.hillje via aroma.affymetrix
<aroma-affymetrix@googlegroups.com> wrote:
> Hey Henrik, first of all thanks for the effort and your help! As you
> suggested, I installed the 'fixed' future package and set future::plan to
> 'eager' and now receive the following message upon fit(cbs):
>
> Error: Something is wrong with the copy-number ratios of sample
> 'GSM1704973,chipEffects' relative to reference
> '.baseline,aa03679a3cdfd0f39ecaf0c9a2c80eeb' on chromosome 1. Too many
> non-finite values: 231306 (100.0% > 20.0%) out of 231306. If this is
> expected, you may adjust argument 'maxNAFraction' when setting up
> CbsModel().
Good to see that the new future no longer hides this true error
message. FYI, future 1.0.1 is now on CRAN, so a regular
update.packages() should give you that.
>
>
> So, all CN ratios are NA, right? If so, I guess the problem is upstream,
> perhaps in one of the normalization steps?
If either the tumor or the normal (or pooled reference) is very noisy,
the above sanity check may trigger an error. However, in those cases,
you wouldn't expect all signals to be non-finite (i.e. all missing).
So it is not obvious to me what's wrong. There could be many reasons
for this. Have a look at the signals from your tumor and your pooled
normal to see if they make sense. I suspect one of them have failed,
either as a bad hyrbidization / array or an incomplete write in the
preprocessing (although I don't see how that should happen because
everything is written atomically). If other tumor vs pooled normals
work, then it is most likely a problem with the tumor sample and not
the pooled normals.
Hope this helps
Henrik
>
> On Saturday, July 2, 2016 at 4:46:26 AM UTC+2, Henrik Bengtsson wrote:
>>
>> Also, install the following version of the future package:
>>
>>
>> source("http://callr.org/install#HenrikBengtsson/future@FutureErrorFix";)
>>
>> This should reveal the true underlying error message.
>>
>> /Henrik
>>
>> On Friday, July 1, 2016 at 11:09:36 AM UTC-7, Henrik Bengtsson wrote:
>>>
>>> Unfortunately, there's a "bug" in future 1.0.0 causing the actual
>>> error to be disguised as "Cannot get static instance. ..."; there
>>> should really be an informative error message, cf.
>>> https://github.com/HenrikBengtsson/future/issues/83.
>>>
>>> But your traceback gives some more information and I see you're using
>>> parallel processing, i.e. you're using:
>>>
>>> plan(multiprocess)
>>>
>>> somewhere at the beginning of your script, correct? As a starter,
>>> could you retry with:
>>>
>>> plan(eager)
>>>
>>> If that works / doesn't work, at least it'll give some more clues
>>> what's going on.
>>>
>>> In the meanwhile, I'll try to fix that future bug causing us not to
>>> see the actual error message. When I've got a working fix, I'll share
>>> a early-access version with you.
>>>
>>> /Henrik
>>>
>>>
>>>
>>> On Fri, Jul 1, 2016 at 8:02 AM, roman.hillje via aroma.affymetrix
>>> <aroma-af...@googlegroups.com> wrote:
>>> > Thanks for the comment. Unfortunately, the error persists even after
>>> > the
>>> > updates. Here is the sessionInfo() output:
>>> >
>>> > R version 3.3.0 (2016-05-03)
>>> >
>>> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> >
>>> > Running under: OS X 10.11.5 (El Capitan)
>>> >
>>> >
>>> > locale:
>>> >
>>> > [1] C/UTF-8/C/C/C/C
>>> >
>>> >
>>> > attached base packages:
>>> >
>>> > [1] stats graphics grDevices utils datasets methods base
>>> >
>>> >
>>> > other attached packages:
>>> >
>>> > [1] DNAcopy_1.46.0 aroma.light_3.2.0
>>> > aroma.affymetrix_3.0.0
>>> >
>>> > [4] aroma.core_3.0.0 R.devices_2.14.0 R.filesets_2.10.0
>>> >
>>> > [7] R.utils_2.3.0 R.oo_1.20.0 affxparser_1.44.0
>>> >
>>> > [10] R.methodsS3_1.7.1 sfit_0.3.0
>>> >
>>> >
>>> > loaded via a namespace (and not attached):
>>> >
>>> > [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0
>>> > future_1.0.0
>>> >
>>> > [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0
>>> > tools_3.3.0
>>> >
>>> > [9] R.cache_0.12.0 parallel_3.3.0 base64enc_0.1-3
>>> > aroma.apd_0.6.0
>>> >
>>> > [13] R.rsp_0.30.0 globals_0.6.1
>>> >
>>> >
>>> > I tried running fit(cbs) - which I'm sure is the same getRegions()
>>> > would do
>>> > ultimately. Here are the error messages and the traceback:
>>> >
>>> > fit(cbs)
>>> >
>>> >
>>> > Attaching package: ‘future’
>>> >
>>> >
>>> > The following object is masked from ‘package:R.utils’:
>>> >
>>> >
>>> > %<-%
>>> >
>>> >
>>> >
>>> > Attaching package: ‘future’
>>> >
>>> >
>>> > The following object is masked from ‘package:R.utils’:
>>> >
>>> >
>>> > %<-%
>>> >
>>> >
>>> >
>>> > Attaching package: ‘future’
>>> >
>>> >
>>> > The following object is masked from ‘package:R.utils’:
>>> >
>>> >
>>> > %<-%
>>> >
>>> >
>>> >
>>> > Attaching package: ‘future’
>>> >
>>> >
>>> > The following object is masked from ‘package:R.utils’:
>>> >
>>> >
>>> > %<-%
>>> >
>>> >
>>> >
>>> > Attaching package: ‘future’
>>> >
>>> >
>>> > The following object is masked from ‘package:R.utils’:
>>> >
>>> >
>>> > %<-%
>>> >
>>> >
>>> > Error in getStaticInstance.Object(this) :
>>> >
>>> > Cannot get static instance. Failed to locate Class object for class
>>> > 'FutureError'.
>>> >
>>> >
>>> > traceback:
>>> >
>>> >
>>> > 24: stop("Cannot get static instance. Failed to locate Class object for
>>> > class '",
>>> >
>>> > className, "'.")
>>> >
>>> > 23: getStaticInstance.Object(this)
>>> >
>>> > 22: getStaticInstance(this)
>>> >
>>> > 21: .getStaticInstance(this, static = static)
>>> >
>>> > 20: `$.Object`(c, "message")
>>> >
>>> > 19: c$message
>>> >
>>> > 18: conditionMessage.condition(cond)
>>> >
>>> > 17: conditionMessage(cond)
>>> >
>>> > 16: stop(FutureError(value, future = future))
>>> >
>>> > 15: value.Future(future)
>>> >
>>> > 14: NextMethod("value")
>>> >
>>> > 13: value.MulticoreFuture(future)
>>> >
>>> > 12: value(future)
>>> >
>>> > 11: eval(expr, envir, enclos)
>>> >
>>> > 10: eval(quote({
>>> >
>>> > value <- value(future)
>>> >
>>> > rm(list = future_name, envir = assign.env)
>>> >
>>> > value
>>> >
>>> > }), new.env())
>>> >
>>> > 9: eval(expr, envir, enclos)
>>> >
>>> > 8: eval(expr, p)
>>> >
>>> > 7: eval.parent(substitute(eval(quote(expr), envir)))
>>> >
>>> > 6: local({
>>> >
>>> > value <- value(future)
>>> >
>>> > rm(list = future_name, envir = assign.env)
>>> >
>>> > value
>>> >
>>> > })
>>> >
>>> > 5: mget(vars[ok], envir = x, inherits = FALSE)
>>> >
>>> > 4: as.list.listenv(res)
>>> >
>>> > 3: as.list(res)
>>> >
>>> > 2: fit.CopyNumberSegmentationModel(cbs)
>>> >
>>> > 1: fit(cbs)
>>> >
>>> >
>>> > I think it's pretty obvious that simply the xdr-files are missing, I
>>> > just
>>> > don't know why.
>>> >
>>> > On Friday, July 1, 2016 at 4:34:22 PM UTC+2, Henrik Bengtsson wrote:
>>> >>
>>> >> Quick comment: Make sure all your packages are up-to-date and retry.
>>> >> If that doesn't work, please post your sessionInfo() after you get the
>>> >> error.
>>> >>
>>> >> /Henrik
>>> >>
>>> >> On Wed, Jun 29, 2016 at 1:32 AM, roman.hillje via aroma.affymetrix
>>> >> <aroma-af...@googlegroups.com> wrote:
>>> >> > Hi,
>>> >> >
>>> >> > I'm currently trying to set up the analysis of CytoScanHD arrays
>>> >> > through
>>> >> > the
>>> >> > aroma pipeline but ran into an issue with the CbsModel function. I
>>> >> > prepared
>>> >> > my sample and reference set so that I end up with this:
>>> >> >
>>> >> > sample set:
>>> >> >
>>> >> > CnChipEffectSet:
>>> >> >
>>> >> > Name: GSE69632
>>> >> >
>>> >> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>>> >> >
>>> >> > Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>>> >> >
>>> >> > Platform: Affymetrix
>>> >> >
>>> >> > Chip type: CytoScanHD_Array,monocell
>>> >> >
>>> >> > Number of arrays: 5
>>> >> >
>>> >> > Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991
>>> >> > [5]
>>> >> >
>>> >> > Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
>>> >> >
>>> >> > Total file size: 173.14MB
>>> >> >
>>> >> > RAM: 0.01MB
>>> >> >
>>> >> > Parameters: {}
>>> >> >
>>> >> >
>>> >> > reference set:
>>> >> >
>>> >> >
>>> >> > CnChipEffectSet:
>>> >> >
>>> >> > Name: referenceSet
>>> >> >
>>> >> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>>> >> >
>>> >> > Path:
>>> >> > plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>>> >> >
>>> >> > Platform: Affymetrix
>>> >> >
>>> >> > Chip type: CytoScanHD_Array,monocell
>>> >> >
>>> >> > Number of arrays: 5
>>> >> >
>>> >> > Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
>>> >> >
>>> >> > Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
>>> >> >
>>> >> > Total file size: 173.14MB
>>> >> >
>>> >> > RAM: 0.01MB
>>> >> >
>>> >> > Parameters: {}
>>> >> >
>>> >> >
>>> >> > Then I do 'cbs <- CbsModel(sampleSet, referenceSet)' and get the
>>> >> > following
>>> >> > output:
>>> >> >
>>> >> >
>>> >> > CbsModel:
>>> >> >
>>> >> > Name: GSE69632
>>> >> >
>>> >> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B,paired
>>> >> >
>>> >> > Chip type (virtual): CytoScanHD_Array
>>> >> >
>>> >> > Path:
>>> >> > cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array
>>> >> >
>>> >> > Number of chip types: 1
>>> >> >
>>> >> > Sample & reference file pairs:
>>> >> >
>>> >> > Chip type #1 ('CytoScanHD_Array') of 1:
>>> >> >
>>> >> > Sample data set:
>>> >> >
>>> >> > CnChipEffectSet:
>>> >> >
>>> >> > Name: GSE69632
>>> >> >
>>> >> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>>> >> >
>>> >> > Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>>> >> >
>>> >> > Platform: Affymetrix
>>> >> >
>>> >> > Chip type: CytoScanHD_Array,monocell
>>> >> >
>>> >> > Number of arrays: 5
>>> >> >
>>> >> > Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991
>>> >> > [5]
>>> >> >
>>> >> > Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
>>> >> >
>>> >> > Total file size: 173.14MB
>>> >> >
>>> >> > RAM: 0.01MB
>>> >> >
>>> >> > Parameters: {}
>>> >> >
>>> >> > Reference data set/file:
>>> >> >
>>> >> > CnChipEffectSet:
>>> >> >
>>> >> > Name: referenceSet
>>> >> >
>>> >> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
>>> >> >
>>> >> > Path:
>>> >> > plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
>>> >> >
>>> >> > Platform: Affymetrix
>>> >> >
>>> >> > Chip type: CytoScanHD_Array,monocell
>>> >> >
>>> >> > Number of arrays: 5
>>> >> >
>>> >> > Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
>>> >> >
>>> >> > Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
>>> >> >
>>> >> > Total file size: 173.14MB
>>> >> >
>>> >> > RAM: 0.01MB
>>> >> >
>>> >> > Parameters: {}
>>> >> >
>>> >> > RAM: 0.00MB
>>> >> >
>>> >> >
>>> >> > Until here everything is fine, but when trying to run getRegions()
>>> >> > on
>>> >> > the
>>> >> > CbsModel I receive an error:
>>> >> >
>>> >> >
>>> >> > reg <- getRegions(cbs, arrays=1, chromosomes=1:22,
>>> >> > verbose=Arguments$getVerbose(-1))
>>> >> >
>>> >> > Extracting regions from all fits...
>>> >> >
>>> >> > Obtaining CN model fits (or fit if missing)...
>>> >> >
>>> >> > Error in getStaticInstance.Object(this) :
>>> >> >
>>> >> > Cannot get static instance. Failed to locate Class object for
>>> >> > class
>>> >> > 'FutureError'.
>>> >> >
>>> >> > Obtaining CN model fits (or fit if missing)...done
>>> >> >
>>> >> > Extracting regions from all fits...done
>>> >> >
>>> >> >
>>> >> > Does anybody know what the issue could be? I suspect it has to do
>>> >> > with
>>> >> > the
>>> >> > CbsModel because the respective folder
>>> >> >
>>> >> > (cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array)
>>> >> > stays
>>> >> > empty even though attempted to be modified at the time of running
>>> >> > the
>>> >> > getRegions command.
>>> >> >
>>> >> >
>>> >> > I would really appreciate input/feedback/ideas since I'm relatively
>>> >> > new
>>> >> > to
>>> >> > the topic :)
>>> >> >
>>> >> > --
>>> >> > --
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>>> >> > latest
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