HenrikBengtsson
commented
3 years ago Hi. Thanks for reporting.
I can reproduce this. I'll try to fix this.
/Henrik
On Mon, Oct 26, 2020 at 3:22 AM Habu notifications@github.com wrote:
Since i cannot post any new question at https://groups.google.com/forum/?oldui=1#!forum/aroma-affymetrix, I am asking for your help here.
When i tried to run the example(https://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/), an error occurred.
here is the script:
library("aroma.affymetrix") verbose <- Arguments$getVerbose(-10, timestamp=TRUE) dataSet <- "GSE12702" chipType <- "Mapping250K_Nsp" csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType) pair <- c(T="GSM318736", N="GSM318737") csR <- csR[indexOf(csR, pair)] res <- doASCRMAv2(csR, verbose=verbose)
The error:
Exception: Do not know how to unwrap object: AromaUnitTotalCnBinarySet
at #10. extract.default(ass, keep, onDuplicates = "error")
extract.default() is in environment 'R.utils'
at #09. extract(ass, keep, onDuplicates = "error")
extract() is in environment 'R.utils'
at #08. exportTotalAndFracB.SnpChipEffectSet(cesN, verbose = verbose, fields = c("total", "fracB"))
exportTotalAndFracB.SnpChipEffectSet() is in environment 'aroma.affymetrix'
at #07. NextMethod("exportTotalAndFracB", fields = fields)
NextMethod() is in environment 'base'
at #06. exportTotalAndFracB.CnChipEffectSet(cesN, verbose = verbose)
exportTotalAndFracB.CnChipEffectSet() is in environment 'aroma.affymetrix'
at #05. exportTotalAndFracB(cesN, verbose = verbose)
exportTotalAndFracB() is in environment 'aroma.affymetrix'
at #04. doCRMAv2.AffymetrixCelSet(..., combineAlleles = FALSE)
doCRMAv2.AffymetrixCelSet() is in environment 'aroma.affymetrix'
at #03. doCRMAv2(..., combineAlleles = FALSE)
doCRMAv2() is in environment 'aroma.affymetrix'
at #02. doASCRMAv2.default(csR, verbose = verbose)
doASCRMAv2.default() is in environment 'aroma.affymetrix'
at #01. doASCRMAv2(csR, verbose = verbose)
- doASCRMAv2() is in environment 'aroma.affymetrix'
Error: Do not know how to unwrap object: AromaUnitTotalCnBinarySet In addition: Warning messages: 1: In transform(y) : NaNs produced 2: In transform(y) : NaNs produced 3: In (function (...) : NaNs produced
sessionInfo:
sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] aroma.light_3.18.0 aroma.affymetrix_3.2.0 affxparser_1.60.0 aroma.core_3.2.1 R.devices_2.16.1 [6] R.filesets_2.13.0 R.utils_2.10.1 R.oo_1.24.0 R.methodsS3_1.8.1
loaded via a namespace (and not attached): [1] DNAcopy_1.62.0 splines_4.0.2 aroma.apd_0.6.0 R.cache_0.14.0 globals_0.13.1 tools_4.0.2 [7] parallel_4.0.2 R.huge_0.9.0 xfun_0.18 tinytex_0.26 PSCBS_0.65.0 matrixStats_0.57.0 [13] digest_0.6.27 R.rsp_0.44.0 base64enc_0.1-3 codetools_0.2-16 sfit_0.3.1 compiler_4.0.2 [19] future_1.19.1 listenv_0.8.0
traceback:
traceback() 15: stop(cond) 14: throw.Exception(Exception(...)) 13: throw(Exception(...)) 12: throw.default("Do not know how to unwrap object: ", class(x)[1L]) 11: throw("Do not know how to unwrap object: ", class(x)[1L]) 10: extract.default(ass, keep, onDuplicates = "error") 9: extract(ass, keep, onDuplicates = "error") 8: exportTotalAndFracB.SnpChipEffectSet(cesN, verbose = verbose, fields = c("total", "fracB")) 7: NextMethod("exportTotalAndFracB", fields = fields) 6: exportTotalAndFracB.CnChipEffectSet(cesN, verbose = verbose) 5: exportTotalAndFracB(cesN, verbose = verbose) 4: doCRMAv2.AffymetrixCelSet(..., combineAlleles = FALSE) 3: doCRMAv2(..., combineAlleles = FALSE) 2: doASCRMAv2.default(csR, verbose = verbose) 1: doASCRMAv2(csR, verbose = verbose)
file path:
----annotationData----chipTypes----Mapping250K_Nsp---- Mapping250K_Nsp,HB20080710.acs Mapping250K_Nsp,monocell.CDF Mapping250K_Nsp,monocell.CDF.md5 Mapping250K_Nsp,na31,HB20101007.ufl Mapping250K_Nsp,na31,HB20101007.ugp Mapping250K_Nsp,na31,HB20101007.ugp.md5 Mapping250K_Nsp.cdf ----rawData----GSE12702----Mapping250K_Nsp---- GSM318736.CEL GSM318737.CEL
I also tried the CEL files of GenomeWideSNP_6 array with the latest annotation files(GenomeWideSNP_6,Full.cdf, GenomeWideSNP_6,Full,na35,hg19,dbSNP141,HB20170323.ugp, GenomeWideSNP_6,Full,na35,hg19,dbSNP141,HB20170323.ufl, GenomeWideSNP_6,HB20080710.acs), but the same error occurred.
I don't know how to solve this problem, please help me, thanks!
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Since i cannot post any new question at https://groups.google.com/forum/?oldui=1#!forum/aroma-affymetrix, I am asking for your help here.
When i tried to run the example(https://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/), an error occurred.
here is the script:
The error:
sessionInfo:
traceback:
file path:
I also tried the CEL files of GenomeWideSNP_6 array with the latest annotation files(GenomeWideSNP_6,Full.cdf, GenomeWideSNP_6,Full,na35,hg19,dbSNP141,HB20170323.ugp, GenomeWideSNP_6,Full,na35,hg19,dbSNP141,HB20170323.ufl, GenomeWideSNP_6,HB20080710.acs), but the same error occurred.
I don't know how to solve this problem, please help me, thanks!