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." *
*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"
<https://lh3.googleusercontent.com/-BolmlflM140/VpNaxx3h3BI/AAAAAAAAAAM/9jVOdDWKWYw/s1600/%25E6%258D%2595%25E8%258E%25B7.JPG>
Looking forward your replay. Thank you very much.
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