Hi, Henrik My working directory is "Y:/cchen/AS&Methy", so CDF file is in "Y:/cchen/AS&Methy/annotationData/chipTypes/HuGene-1_0-st-v1" and CEL files are at "Y:/cchen/AS&Methy/rawData/tissues/HuGene-1_0-st-v1/"
The unwritable folder is "Y:\cchen\AS&Methy\probeData\tissues,RBC\HuGene-1_0-st-v1", I think it is going to save the background correction data. Although it exists, no files are created in that file. > getwd() [1] "Y:/cchen/AS&Methy" > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets grid utils methods base other attached packages: [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1 matrixStats_0.2.1 [8] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3 digest_0.4.2 GenomeGraphs_1.8.0 biomaRt_2.4.0 FIRMAGene_0.9.5 [15] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0 loaded via a namespace (and not attached): [1] RCurl_1.4-3 tools_2.11.1 XML_3.1-1 On Fri, Sep 3, 2010 at 11:02 AM, Henrik Bengtsson <h...@stat.berkeley.edu>wrote: > Hi, > > Q1. What is your sessionInfo() when the error occurs. > > Q2. What is your working directories, i.e. what does print(getwd()) give? > > /Henrik > > On Fri, Sep 3, 2010 at 8:23 AM, AlexChen <chench...@gmail.com> wrote: > > Hi, > > > > I want to use FIRMAGene package (http://bioinf.wehi.edu.au/folders/ > > firmagene/sup3_04feb2010.R) to analysis alternative splice in my data, > > but got a problem. > > > > here is my code: > > > > library(FIRMAGene) > > library(GenomeGraphs) > > library(aroma.affymetrix) > > verbose <- Arguments$getVerbose(-30); timestampOn(verbose) > > affxparser::convertCdf("./annotationData/chipTypes/HuGene-1_0-st-v1/ > > HuGene-1_0-st-v1.cdf","./annotationData/chipTypes/HuGene-1_0-st-v1/ > > HuGene-1_0-st-v1.cdf") > > cdf<-AffymetrixCdfFile$byChipType("HuGene-1_0-st-v1",verbose=verbose) > > cs<-AffymetrixCelSet$byName("tissues",cdf=cdf,verbose=verbose) > > bc <- RmaBackgroundCorrection(cs) > > > > #works well but... > > csBC <- process(bc,verbose=verbose) > > 20100903 09:54:16|Background correcting data set... > > Error in list(`process(bc, verbose = verbose)` = <environment>, > > `process.RmaBackgroundCorrection(bc, verbose = verbose)` = > > <environment>, : > > > > [2010-09-03 09:54:17] Exception: No write permission for directory: > > probeData/tissues,RBC/HuGene-1_0-st-v1 > > at throw(Exception(...)) > > at throw.default("No write permission for directory: ", path) > > at throw("No write permission for directory: ", path) > > at getWritablePathname.Arguments(static, file = "dummy-not-created", > > path = path, ...) > > at getWritablePathname(static, file = "dummy-not-created", path = > > path, ...) > > at method(static, ...) > > at Arguments$getWritablePath(path) > > at bgAdjustRma.AffymetrixCelSet(NA, path = "probeData/tissues,RBC/ > > HuGene-1_0-st-v1", verbose = TRUE, overwrite = FALSE, subsetToUpdate = > > NULL, typesToUpdate = "pm", addJitter > > at bgAdjustRma(NA, path = "probeData/tissues,RBC/HuGene-1_0-st-v1", > > verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, > > typesToUpdate = "pm", addJitter = FALSE, jitterSd > > at do.call("bgAdjustRma", args = args) > > at process.RmaBackgroundCorrection(bc, verbose = verbose) > > at process(bc, verbose = verbose) > > 20100903 09:54:17|Background correcting data set...done > > > > The folder "probeData/tissues,RBC/HuGene-1_0-st-v1" has been created, > > and indeed writable when I created one new txt file as a test. But the > > no written permission problem is still there. Any suggestions? Thanks > > so much. > > > > -- > > 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/ > > > > -- > 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/ > -- Chen, Chao Psychiatry University of Chicago 924 E 57th St, Chicago, IL 60637 U. S. A. MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University 220# Handan Road, Shanghai (200433) P.R.China -- 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/
