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().*
So, all CN ratios are NA, right? If so, I guess the problem is upstream,
perhaps in one of the normalization steps?
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 <javascript:>> 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 :)
>> >> >
>> >> > --
>> >> > --
>> >> > 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-af...@googlegroups.com
>> >> > To unsubscribe and other options, go to
>> >> > http://www.aroma-project.org/forum/
>> >> >
>> >> > ---
>> >> > You received this message because you are subscribed to the Google
>> >> > Groups
>> >> > "aroma.affymetrix" group.
>> >> > To unsubscribe from this group and stop receiving emails from it,
>> send
>> >> > an
>> >> > email to aroma-affymetr...@googlegroups.com.
>> >> > For more options, visit https://groups.google.com/d/optout.
>> >
>> > --
>> > --
>> > 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-af...@googlegroups.com
>> <javascript:>
>> > To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>> >
>> > ---
>> > You received this message because you are subscribed to the Google
>> Groups
>> > "aroma.affymetrix" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an
>> > email to aroma-affymetr...@googlegroups.com <javascript:>.
>> > For more options, visit https://groups.google.com/d/optout.
>>
>
--
--
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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
