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.comwrote:
> >>
> >> 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
> > "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/.
> 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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