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 email@example.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/