Hi,
thanks for reporting with more details. I see that both of you are
using aroma.core 2.11.1, and it could be that that version is causing
the problem. Try to revert back to aroma.core 2.11.0 (available on
CRAN) as:
install.packages("aroma.core")
Then restart(!) R and retry. Please let me know if this solves it
(because then I'll make sure to not make aroma.core 2.11.1 available
via the current installation scripts).
Henrik
On Sun, Feb 2, 2014 at 9:42 AM, <bibhubioin...@gmail.com> wrote:
>
> Hello,
>
>
> Here is complete details of my code and encountered same problem.
>
>
> After creating Directory structure i have run following codes and got the
> error as follows:
>
> 1. source("http://aroma-project.org/hbLite.R";)
> 2.hbInstall("aroma.cn")
> 3. hbInstall("aroma.affymetrix")
> setwd("D:/Array Express and GEO Files/Aroma-gse11882")
> source("http://bioconductor.org/biocLite.R";)
> biocLite()
> library(aroma.affymetrix) # load aroma.affymetrix package
> library(Biobase) # bioconductor
> library(gplots) # CRAN
> library(gdata) # CRAN
> library(limma) # bioconductor
> library(GenomeGraphs) # bioconductor
> library(affy) # bioconductor
> library(aroma.affymetrix);
> verbose<- Arguments$getVerbose(-8, timestamp=TRUE);
> chipType<- "HG-U133_Plus_2"
> cdf<-
> AffymetrixCdfFile('annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf');
> print(cdf)
>
>
> CdfFile:
> Path: annotationData/chipTypes/HG-U133_Plus_2
> Filename: HG-U133_Plus_2.cdf
> File size: 25.04 MB (26251783 bytes)
> Chip type: HG-U133_Plus_2
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 1164x1164
> Number of cells: 1354896
> Number of units: 54675
> Cells per unit: 24.78
> Number of QC units: 9
>
>
> cs<- AffymetrixCelSet$byPath("rawData/mine/HG-U133_Plus_2/");
>
>> print(cs)
> AffymetrixCelSet:
> Name: mine1
> Tags:
> Path: rawData/mine1/HG-U133_Plus_2
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2
> Number of arrays: 173
> Names: GSM300166, GSM300167, GSM300168, ..., GSM350078 [173]
> Time period: 2005-10-14 14:20:42 -- 2007-10-24 16:31:19
> Total file size: 2235.72MB
> RAM: 0.13MB
>
>
> bc<- RmaBackgroundCorrection(cs);
>
>> print(bc)
> Error in readCelHeader(pathname) :
> Argument 'filename' should be a single file:
>
>
> csBC<- process(bc,verbose=verbose);
>
> 20140201 18:36:30|Background correcting data set...
> Error in readCelHeader(pathname) :
> Argument 'filename' should be a single file:
> 20140201 18:36:35|Background correcting data set...done
>
> 20140201 18:36:30|Background correcting data set...
> Error in readCelHeader(pathname) :
> Argument 'filename' should be a single file:
> 20140201 18:36:35|Background correcting data set...done
>
>
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> 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_1.32.0 matrixStats_0.8.14 aroma.affymetrix_2.11.1
> [4] affxparser_1.34.0 aroma.core_2.11.3 R.devices_2.8.2
> [7] R.filesets_2.3.0 R.utils_1.29.8 R.oo_1.17.0
> [10] R.methodsS3_1.6.1 BiocInstaller_1.12.0
>
> 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_0.9.0 R.huge_0.6.0 R.rsp_0.9.28
> [9] tools_3.0.2
>
>> traceback()
> 27: stop("Argument 'filename' should be a single file: ", paste(filename,
> collapse = ", "))
> 26: readCelHeader(pathname)
> 25: getHeader.AffymetrixCelFile(this)
> 24: getHeader(this)
> 23: getCdf.AffymetrixCelFile(getOneFile(this), ...)
> 22: getCdf(getOneFile(this), ...)
> 21: getCdf.AffymetrixCelSet(this)
> 20: getCdf(this)
> 19: clearCache.AffymetrixCelSet(object)
> 18: clearCache(object)
> 17: clone.GenericDataFileSet(this, clear = TRUE, verbose = FALSE)
> 16: NextMethod("clone", clear = TRUE, verbose = less(verbose))
> 15: clone.AffymetrixCelSet(this)
> 14: clone(this)
> 13: extract.GenericDataFileSet(dsOut, fullnames, onMissing = onMissing)
> 12: extract(dsOut, fullnames, onMissing = onMissing)
> 11: getOutputDataSet.AromaTransform(this, incomplete = TRUE, ...,
> verbose = less(verbose, 5), cdf = NA, checkChipType = FALSE)
> 10: NextMethod(generic = "getOutputDataSet", NA, incomplete = TRUE,
> cdf = NA, checkChipType = FALSE, verbose = FALSE)
> 9: do.call("NextMethod", args)
> 8: getOutputDataSet.Transform(this, incomplete = TRUE, ..., verbose =
> less(verbose,
> 5))
> 7: getOutputDataSet(this, incomplete = TRUE, ..., verbose = less(verbose,
> 5))
> 6: findFilesTodo.AromaTransform(this, ...)
> 5: findFilesTodo(this, ...)
> 4: isDone.AromaTransform(this)
> 3: isDone(this)
> 2: process.RmaBackgroundCorrection(bc, verbose = verbose)
> 1: process(bc, verbose = verbose)
>
> Regards,
> Bibhu
> On Friday, January 31, 2014 1:54:20 PM UTC+5:30, bibhub...@gmail.com 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 Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
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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/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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