Thank you Bibhu, this is helpful. Until the next main release of the
Aroma Framework, I'll try to have hbInstall("aroma.affymetrix") to
avoid picking up the wrong aroma.core version.
/Henrik
On Mon, Feb 3, 2014 at 10:06 AM, bibhu prasad <bibhubioin...@gmail.com> wrote:
> Hi,
>
>
>
> aroma.core 2.11.0 is working fine. Thnaks a Lot
>
>
>
> Regards,
>
> Bibhu
>
>
>
> On Mon, Feb 3, 2014 at 12:04 AM, Henrik Bengtsson
> <henrik.bengts...@aroma-project.org> wrote:
>>
>> 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
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>> > "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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>>
>> --
>> --
>> 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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>
>
> --
> --
> 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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--
--
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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