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-affymetrix@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-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.
--
--
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.
