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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