$byChipType(chipType)
print(cdf)
cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
print(cs)
bc <- RmaBackgroundCorrection(cs, tag="coreR2")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
print(qn)
csN <- process(qn, verbose=verbose)
I get stuck at this point. I keep gettng an error
[2010-11-10 09:16:33] Exception: No write permission for directory:
probeData/tissues,coreR2,QN
at throw(Exception(...))
at throw.default("No write permission for directory: ", path)
at throw("No write permission for directory: ", path)
at method(static, ...)
at Arguments$getWritablePathname(path)
at normalizeQuantile.AffymetrixCelFile(df, path = path,
subsetToUpdate = subse
at normalizeQuantile(df, path = path, subsetToUpdate =
subsetToUpdate, typesTo
at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
at do.call("normalizeQuantile", args = args)
at process.QuantileNormalization(qn, verbose = verbose)
at process(qn, verbose = verbose)
In addition: Warning messages:
1: In writeBin(con = con, rawAll) : problem writing to connection
2: In writeBin(con = con, rawAll) : problem writing to connection
3: In fileAccess.default(pathT, mode = 2) :
file.access(..., mode=2) and file(..., open="ab") gives different
results (0 != -1). Will use the file() results: probeData/
tissues,coreR2,QN/K
20101110 09:17:22| Array #2...done
20101110 09:17:22| Normalizing 30 arrays...done
20101110 09:17:22| Normalizing data towards target distribution...done
20101110 09:17:22|Quantile normalizing data set...done
I did get a similar error for csBC <- process(bc,verbose=verbose), but
i fixed it by giving universal write permission n the probeData
folder. But this didn't work for csN <- process(qn, verbose=verbose).
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.6.1 aroma.affymetrix_1.7.3 aroma.apd_0.1.7
[4] affxparser_1.18.0 R.huge_0.2.0 aroma.core_1.7.4
[7] aroma.light_1.18.2 matrixStats_0.2.2 R.rsp_0.4.0
[10] R.cache_0.3.0 R.filesets_0.9.0 digest_0.4.2
[13] R.utils_1.5.6 R.oo_1.7.4 affy_1.24.2
[16] R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1
> traceback()
No traceback available
I did follow a previous forum message regarding a similar problem and
get the following outputs.
> library("R.utils");
> path <- "/home/elsa/probeData/tissues,coreR2,
annotationData/ .cshrc probeData/ .Rcache/
.bash_history .login rawData/ .ssh/
> path <- "/home/elsa/probeData/tissues,coreR2,
annotationData/ .cshrc probeData/ .Rcache/
.bash_history .login rawData/ .ssh/
> path <- "/home/elsa/probeData/tissues,coreR2,QN
+ "
> path <- "/home/elsa/probeData/tissues,coreR2,QN"
> print(path)
[1] "/home/elsa/probeData/tissues,coreR2,QN"
> str(file.info(path));
'data.frame': 1 obs. of 10 variables:
$ size : num 3
$ isdir : logi TRUE
$ mode :Class 'octmode' int 1535
$ mtime : POSIXct, format: "2010-11-10 09:15:13"
$ ctime : POSIXct, format: "2010-11-10 09:16:37"
$ atime : POSIXct, format: "2010-11-10 09:16:37"
$ uid : int 341178
$ gid : int 341178
$ uname : chr "elsa"
$ grname: chr "elsa"
> print(file.access(path, mode=0));
/home/elsa/probeData/tissues,coreR2,QN
0
> print(file.access(path, mode=1));
/home/elsa/probeData/tissues,coreR2,QN
0
> print(file.access(path, mode=2));
/home/elsa/probeData/tissues,coreR2,QN
0
> print(file.access(path, mode=4));
/home/elsa/probeData/tissues,coreR2,QN
0
> print(fileAccess(path,mode=0));
[1] 0
> print(fileAccess(path,mode=1));
[1] 0
> print(fileAccess(path,mode=2));
[1] -1
Warning message:
In fileAccess.default(path, mode = 2) :
file.access(..., mode=2) and file(..., open="ab") gives different
results (0 != -1). Will use the file() results: /home/elsa/probeData/
tissues,coreR2,QN/B
> print(fileAccess(path,mode=4));
[1] 0
> print(isDirectory(path));
[1] TRUE
> print(isFile(path));
[1] FALSE
Looks like R.util does not have write permissions on the folder. I am
just not sure how i ca fix this problem.
Any help is very much appreciated.
Regards
Elsa Chacko
PhD student
Macquarie University
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