Hello,
I am a new user and am encountering the same error.
I believe the following commands run without issue:
#Load analysis library.
library("aroma.affymetrix")
#File I/O.
#Load description file.
cdf = AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
print(cdf)
#Load sequence file.
acs= AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
print(acs)
#Get genome information.
gi=getGenomeInformation(cdf)
print(gi)
#Get SNP information.
si=getSnpInformation(cdf)
print(si)
#Load .CEL files.
csR = AffymetrixCelSet$byName("GSE13372", cdf=cdf)
print(csR)
However, an attempt to call:
AllelicCrosstalkCalibration(cs)
or:
doCRMAv2(("GSE13372",chipType="GenomeWideSNP_6,Full")
Gives the following error:
Error in readCelHeader(pathname) :
Argument 'filename' should be a single file:
Here is the output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_1.32.0 matrixStats_0.8.14 aroma.affymetrix_2.11.1
[4] aroma.core_2.11.3 R.devices_2.8.2 R.filesets_2.3.0
[7] R.utils_1.29.8 R.oo_1.17.0 affxparser_1.34.0
[10] R.methodsS3_1.6.1
loaded via a namespace (and not attached):
[1] aroma.apd_0.4.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.36.0
[5] PSCBS_0.40.3 R.cache_0.9.2 R.huge_0.6.0 R.rsp_0.9.28
[9] tools_3.0.2
Please let me know if you require any additional information. Thank you
very much for your time.
Best,
Colin
On Friday, January 31, 2014 3:34:31 AM UTC-5, Pierre Neuvial wrote:
>
> Hi,
>
> Could you also send a code example that generated this error ? From
> what you sent there is no way to know what you did that generated this
> error.
>
> Best,
>
> Pierre
>
> On Fri, Jan 31, 2014 at 9:24 AM, <bibhub...@gmail.com <javascript:>>
> wrote:
> > Hello sir,
> >
> > i am getting following error. i am giving session info() and traceback
> ()
> > i have tried many option..differrnt system and file name but all failed
> > Please help me .Previously i was able to run sucessfully . But now i am
> > facing the problem
> >
> >> traceback()
> > 31: stop("Argument 'filename' should be a single file: ",
> paste(filename,
> > collapse = ", "))
> > 30: readCelHeader(pathname)
> > 29: getHeader.AffymetrixCelFile(this)
> > 28: getHeader(this)
> > 27: getCdf.AffymetrixCelFile(getOneFile(this), ...)
> > 26: getCdf(getOneFile(this), ...)
> > 25: getCdf.AffymetrixCelSet(this)
> > 24: getCdf(this)
> > 23: clearCache.AffymetrixCelSet(object)
> > 22: clearCache(object)
> > 21: clone.GenericDataFileSet(this, clear = TRUE, verbose = FALSE)
> > 20: NextMethod("clone", clear = TRUE, verbose = less(verbose))
> > 19: clone.AffymetrixCelSet(this)
> > 18: clone(this)
> > 17: extract.GenericDataFileSet(dsOut, fullnames, onMissing = onMissing)
> > 16: extract(dsOut, fullnames, onMissing = onMissing)
> > 15: getOutputDataSet.AromaTransform(this, incomplete = TRUE, ...,
> > verbose = less(verbose, 5), cdf = NA, checkChipType = FALSE)
> > 14: NextMethod(generic = "getOutputDataSet", NA, incomplete = TRUE,
> > cdf = NA, checkChipType = FALSE, verbose = FALSE)
> > 13: do.call("NextMethod", args)
> > 12: getOutputDataSet.Transform(this, incomplete = TRUE, ..., verbose =
> > less(verbose,
> > 5))
> > 11: getOutputDataSet(this, incomplete = TRUE, ..., verbose =
> less(verbose,
> > 5))
> > 10: findFilesTodo.AromaTransform(this, ...)
> > 9: findFilesTodo(this, ...)
> > 8: isDone.AromaTransform(this)
> > 7: isDone(this)
> > 6: sprintf("Is done: %s", isDone(this))
> > 5: as.character.AromaTransform(x)
> > 4: as.character(x)
> > 3: print(as.character(x))
> > 2: print.Object(NA)
> > 1: print(NA)
> >> rs
> > Error: object 'rs' not found
> >> sessionInfo()
> > R version 3.0.2 (2013-09-25)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
> > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
> > [5] LC_TIME=English_India.1252
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] aroma.light_1.32.0 matrixStats_0.8.14
> aroma.affymetrix_2.11.1
> > [4] aroma.core_2.11.3 R.devices_2.8.2 R.filesets_2.3.0
> > [7] R.utils_1.29.1 R.oo_1.17.0 affxparser_1.34.0
> > [10] R.methodsS3_1.6.1
> >
> > loaded via a namespace (and not attached):
> > [1] aroma.apd_0.4.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.36.0
> > [5] PSCBS_0.40.3 R.cache_0.9.2 R.huge_0.6.0 R.rsp_0.9.28
> > [9] tools_3.0.2
> >>
> >
> > --
> > --
> > 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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--
--
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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