hello,have you solved your problem? I met the same error
在 2017年11月14日星期二 UTC+8上午8:29:07，ali jan写道：
>
> I tried your suggestion but it is still not working:
>
> > log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> > # Don't display too many decimals.
> > options(digits=4)
> >
> > cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> > print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/CytoScanHD_Array
> Filename: CytoScanHD_Array.cdf
> File size: 612.27 MiB (642007896 bytes)
> Chip type: CytoScanHD_Array
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 2822125
> Cells per unit: 2.44
> Number of QC units: 4
> >
> > gi <- getGenomeInformation(cdf)
> > print(gi)
> UgpGenomeInformation:
> Name: CytoScanHD_Array
> Tags: na32,hg19,HB20111108
> Full name: CytoScanHD_Array,na32,hg19,HB20111108
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ugp
> File size: 13.46 MiB (14111425 bytes)
> Chip type: CytoScanHD_Array
> >
> > si <- getSnpInformation(cdf)
> > print(si)
> UflSnpInformation:
> Name: CytoScanHD_Array
> Tags: na32,hg19,HB20111108
> Full name: CytoScanHD_Array,na32,hg19,HB20111108
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ufl
> File size: 5.38 MiB (5645047 bytes)
> Chip type: CytoScanHD_Array
> Number of enzymes: 1
> >
> > acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> > print(acs)
> AromaCellSequenceFile:
> Name: CytoScanHD_Array
> Tags: HB20111008
> Full name: CytoScanHD_Array,HB20111008
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
> File size: 170.92 MiB (179217487 bytes)
> Number of data rows: 6892960
> File format: v1
> Dimensions: 6892960x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: <createdOn>20111108 21:44:22
> PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik
>
> Bengtsson</fullname><email>henrik.bengts...@aroma-project.org
> <javascript:></email></createdBy>
> Chip type: CytoScanHD_Array
> Platform: Affymetrix
> >
> > csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> > print(csR)
> AffymetrixCelSet:
> Name: CNV
> Tags:
> Path: rawData/CNV/CytoScanHD_Array
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
> Number of arrays: 460
> Names: GSM1317174_H050150N-CytoScanHD_515-H050150N,
> GSM1317175_H050150T-CytoScanHD_516-H050150T,
> GSM1317176_H050154N-CytoScanHD_521-H050154N, ...,
> GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
> Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
> Total file size: 29.55 GiB
> >
> > cs <- csR
> > par(mar=c(4,4,1,1)+0.1)
> > plotDensity(cs, lwd=2, ylim=c(0,0.40))
>
> > acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> > print(acc)
> AllelicCrosstalkCalibration:
> Data set: CNV
> Input tags:
> User tags: *
> Asterisk ('*') tags: ACC,ra,-XY
> Output tags: ACC,ra,-XY
> Number of files: 460 (29.55 GiB)
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
> Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200,
> subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi
> TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$
> alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num
> 2, ..$ Q: num 98}
> Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
> Is done: FALSE
> > print(csC)
> Error in print(csC) : object 'csC' not found
> > sessionInfo()
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_3.8.0 aroma.affymetrix_3.1.0 aroma.core_3.1.1
> R.devices_2.15.1 R.filesets_2.11.0 R.utils_2.5.0
> [7] R.oo_1.21.0 affxparser_1.50.0 R.methodsS3_1.7.1
>
> loaded via a namespace (and not attached):
> [1] matrixStats_0.52.2 codetools_0.2-15 listenv_0.6.0 future_1.6.2
> digest_0.6.12 R.huge_0.9.0 PSCBS_0.63.0
> [8] tools_3.4.2 R.cache_0.12.0 parallel_3.4.2
> compiler_3.4.2 base64enc_0.1-3 aroma.apd_0.6.0 R.rsp_0.41.0
> [15] globals_0.10.3 DNAcopy_1.52.0
> > traceback()
> No traceback available
>
> On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson
> wrote:
>>
>> On Sun, Jan 10, 2016 at 11:36 PM, <wxp...@gmail.com> wrote:
>> >
>> > Hi dear professor Henrik Bengtsson,
>> >
>> > When I was declaring the raw data set of CytoScan HD Array with
>> aroma.affymetrix, I'm encountering the following errors:
>> >
>> > "Error: object 'csC' not found."
>>
>> It seems like you didn't run the command before. Make sure each
>> object is actually created in every step by printing it, e.g.
>> print(cdf), etc. That should help you narrow down where your problem
>> is.
>>
>> /Henrik
>>
>> >
>> > I have searched the forum, unfortunately, I can't solve this problem.
>> >
>> > Could you give me some suggestions and help me solve it ?
>> >
>> > The following are the R code of mine:
>> >
>> > > setwd("G:/")
>> >
>> > >library("aroma.affymetrix")
>> >
>> > >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> >
>> > >options(digits=4)
>> >
>> > >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>> >
>> > >gi <- getGenomeInformation(cdf)
>> >
>> > >si <- getSnpInformation(cdf)
>> >
>> > >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>> >
>> > >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>> >
>> > >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>> >
>> > >csC <- process(acc, verbose=verbose)
>> >
>> > > print(csC)
>> >
>> > > sessionInfo()
>> > R version 3.2.2 (2015-08-14)
>> > Platform: x86_64-w64-mingw32/x64 (64-bit)
>> > Running under: Windows 7 x64 (build 7601) Service Pack 1
>> >
>> > locale:
>> > [1] LC_COLLATE=English_United States.1252
>> > [2] LC_CTYPE=English_United States.1252
>> > [3] LC_MONETARY=English_United States.1252
>> > [4] LC_NUMERIC=C
>> > [5] LC_TIME=English_United States.1252
>> >
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods base
>> >
>> > other attached packages:
>> > [1] aroma.light_2.4.0 aroma.affymetrix_2.14.0 affxparser_1.42.0
>> > [4] aroma.core_3.0.0 R.devices_2.13.2 R.filesets_2.10.0
>> > [7] R.utils_2.2.0 R.oo_1.19.0 R.methodsS3_1.7.0
>> >
>> > loaded via a namespace (and not attached):
>> >
>> > [1] matrixStats_0.50.1 codetools_0.2-14 listenv_0.6.0
>> future_0.10.0
>> > [5] digest_0.6.8 R.huge_0.9.0 PSCBS_0.60.0
>> tools_3.2.2
>> > [9] R.cache_0.12.0 parallel_3.2.2 base64enc_0.1-3
>> aroma.apd_0.6.0
>> > [13] R.rsp_0.21.0 globals_0.6.0 DNAcopy_1.42.0
>> >
>> > CEL format raw data are locate in
>> "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>> >
>> > Looking forward your replay. Thank you very much.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > --
>> > 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
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>> >
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>>
>
--
--
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.
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