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/ > > > > --- > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to aroma-affymetrix+unsubscr...@googlegroups.com. > > For more options, visit https://groups.google.com/groups/opt_out. > > -- > -- > 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/ > > --- > You received this message because you are subscribed to a topic in the > Google Groups "aroma.affymetrix" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/aroma-affymetrix/f1Du8FH4--s/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.