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.
>
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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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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