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/
