Re: [aroma.affymetrix] Error in readCelHeader(pathname) : Argument 'filename' should be a single file ..

2014-01-31 Thread Pierre Neuvial 
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,   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_0.6.4DNAcopy_1.36.0
> [5] PSCBS_0.40.3R.cache_0.9.2   R.huge_0.6.0R.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.
>
>
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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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Re: [aroma.affymetrix] Error in readCelHeader(pathname) : Argument 'filename' should be a single file ..

2014-02-02 Thread cwaters1 
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-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_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_0.6.4DNAcopy_1.36.0 
[5] PSCBS_0.40.3R.cache_0.9.2   R.huge_0.6.0R.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,  > 
> 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):