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.
--
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